prd Schema

• Primary Key: prd_id
• Tables: 17

brief_summary

Column	Type	Description
prd_id	text	PRDID of an entry. All tables/categories refer back to the PRDID in the brief_summary table.
docid	bigint	Serial counter (unique integer) to represent the row id.
name	text
formula	text
description	text
pdbx_initial_date	date	Inclusion date to the PDB of an entry
pdbx_modified_date	date	Modification date of an entry
update_date	timestamp without time zone	Entry update date (within the RDB).
canonical_smiles	text	[pmb] Canonical SMILES string generated from PRDCC block via ccd2rdmol
chem_comp_id	text	[pmb] Chemical component ID linking to cc.brief_summary (from pdbx_reference_molecule)
keywords	text[]	Array of keywords.

RDKit Integration

The prd pipeline automatically sets up RDKit PostgreSQL Cartridge for chemical structure searching, similar to the cc schema. This includes:

1. RDKit extension (CREATE EXTENSION IF NOT EXISTS rdkit)
2. mol column on prd.brief_summary -- stores RDKit molecule objects generated from canonical SMILES
3. GiST index on mol for fast substructure and similarity searches
4. RDKit descriptor columns -- rdkit_mw, rdkit_logp, rdkit_tpsa, rdkit_hba, rdkit_hbd, rdkit_rotbonds, rdkit_rings, rdkit_formula

To set up RDKit on an existing database:

pixi run pmb setup-rdkit

Example Queries

-- Find PRD entries by substructure
SELECT prd_id, name FROM prd.brief_summary WHERE mol @> 'c1ccccc1'::mol;

-- PRD entries with molecular weight > 500
SELECT prd_id, name, rdkit_mw FROM prd.brief_summary
WHERE rdkit_mw > 500 ORDER BY rdkit_mw DESC;

SMILES Coverage

SMILES are generated from PRDCC files (the _chem_comp_atom / _chem_comp_bond data). Coverage depends on how the molecule is represented in wwPDB:

represent_as	Entries	SMILES in prd.brief_summary	Reason
polymer	~649	Yes	PRDCC file exists with full atom/bond data
branched	~153	Yes	PRDCC file exists with full atom/bond data
single molecule	~373	No	No PRDCC file -- structure is defined by a single CCD entry

"single molecule" entries are PRDs whose structure is fully described by one CCD component (chem_comp_id in pdbx_reference_molecule). wwPDB does not generate separate PRDCC files for these because the structure already exists in CCD. Their SMILES can be found via the linked CCD entry:

-- Get SMILES for single-molecule PRDs via CCD
SELECT bs.prd_id, pm.chem_comp_id, cc.canonical_smiles
FROM prd.brief_summary bs
JOIN prd.pdbx_reference_molecule pm USING (prd_id)
JOIN cc.brief_summary cc ON pm.chem_comp_id = cc.comp_id
WHERE bs.canonical_smiles IS NULL;

tip

The chem.compounds table combines both sources, so you can search all compounds (cc + prd) with SMILES in one place without worrying about this distinction.

chem_comp

Column	Type	Description
prd_id	text	PRDID of an entry. All tables/categories refer back to the PRDID in the brief_summary table.
formula	text	The formula for the chemical component. Formulae are written according to the following rules: (1) Only recognized element symbols may be used. (2) Each element symbol is followed by a 'count' number. A count of '1' may be omitted. (3) A space or parenthesis must separate each cluster of (element symbol + count), but in general parentheses are not used. (4) The order of elements depends on whether carbon is present or not. If carbon is present, the order should be: C, then H, then the other elements in alphabetical order of their symbol. If carbon is not present, the elements are listed purely in alphabetic order of their symbol. This is the 'Hill' system used by Chemical Abstracts.
formula_weight	double precision	Formula mass in daltons of the chemical component.
id	text	The value of _chem_comp.id must uniquely identify each item in the CHEM_COMP list. For protein polymer entities, this is the three-letter code for the amino acid. For nucleic acid polymer entities, this is the one-letter code for the base.
name	text	The full name of the component.
type	text	For standard polymer components, the type of the monomer. Note that monomers that will form polymers are of three types: linking monomers, monomers with some type of N-terminal (or 5') cap and monomers with some type of C-terminal (or 3') cap.
pdbx_release_status	text	This data item holds the current release status for the component.

chem_comp_atom

Column	Type	Description
prd_id	text	PRDID of an entry. All tables/categories refer back to the PRDID in the brief_summary table.
alt_atom_id	text	An alternative identifier for the atom. This data item would be used in cases where alternative nomenclatures exist for labelling atoms in a group.
atom_id	text	The value of _chem_comp_atom.atom_id must uniquely identify each atom in each monomer in the CHEM_COMP_ATOM list. The atom identifiers need not be unique over all atoms in the data block; they need only be unique for each atom in a component. Note that this item need not be a number; it can be any unique identifier.
charge	integer	The net integer charge assigned to this atom. This is the formal charge assignment normally found in chemical diagrams.
model_Cartn_x	double precision	The x component of the coordinates for this atom in this component specified as orthogonal angstroms. The choice of reference axis frame for the coordinates is arbitrary. The set of coordinates input for the entity here is intended to correspond to the atomic model used to generate restraints for structure refinement, not to atom sites in the ATOM_SITE list.
model_Cartn_y	double precision	The y component of the coordinates for this atom in this component specified as orthogonal angstroms. The choice of reference axis frame for the coordinates is arbitrary. The set of coordinates input for the entity here is intended to correspond to the atomic model used to generate restraints for structure refinement, not to atom sites in the ATOM_SITE list.
model_Cartn_z	double precision	The z component of the coordinates for this atom in this component specified as orthogonal angstroms. The choice of reference axis frame for the coordinates is arbitrary. The set of coordinates input for the entity here is intended to correspond to the atomic model used to generate restraints for structure refinement, not to atom sites in the ATOM_SITE list.
comp_id	text	This data item is a pointer to _chem_comp.id in the CHEM_COMP category.
type_symbol	text	The code used to identify the atom species representing this atom type. Normally this code is the element symbol.
pdbx_align	integer	Atom name alignment offset in PDB atom field.
pdbx_ordinal	integer	Ordinal index for the component atom list.
pdbx_component_atom_id	text	The atom identifier in the subcomponent where a larger component has been divided subcomponents.
pdbx_component_comp_id	text	The component identifier for the subcomponent where a larger component has been divided subcomponents.
pdbx_model_Cartn_x_ideal	double precision	An alternative x component of the coordinates for this atom in this component specified as orthogonal angstroms.
pdbx_model_Cartn_y_ideal	double precision	An alternative y component of the coordinates for this atom in this component specified as orthogonal angstroms.
pdbx_model_Cartn_z_ideal	double precision	An alternative z component of the coordinates for this atom in this component specified as orthogonal angstroms.
pdbx_stereo_config	text	The chiral configuration of the atom that is a chiral center.
pdbx_aromatic_flag	text	A flag indicating an aromatic atom.
pdbx_leaving_atom_flag	text	A flag indicating a leaving atom.
pdbx_residue_numbering	integer	Preferred residue numbering in the BIRD definition.
pdbx_polymer_type	text	Is the atom in a polymer or non-polymer subcomponent in the BIRD definition.
pdbx_ref_id	text	A reference to _pdbx_reference_entity_list.ref_entity_id
pdbx_component_id	integer	A reference to _pdbx_reference_entity_list.component_id
pdbx_backbone_atom_flag	text	A flag indicating the backbone atoms in polypeptide units.
pdbx_n_terminal_atom_flag	text	A flag indicating the N-terminal group atoms in polypeptide units.
pdbx_c_terminal_atom_flag	text	A flag indicating the C-terminal group atoms in polypeptide units.

chem_comp_bond

Column	Type	Description
prd_id	text	PRDID of an entry. All tables/categories refer back to the PRDID in the brief_summary table.
atom_id_1	text	The ID of the first of the two atoms that define the bond. This data item is a pointer to _chem_comp_atom.atom_id in the CHEM_COMP_ATOM category.
atom_id_2	text	The ID of the second of the two atoms that define the bond. This data item is a pointer to _chem_comp_atom.atom_id in the CHEM_COMP_ATOM category.
comp_id	text	This data item is a pointer to _chem_comp.id in the CHEM_COMP category.
value_order	text	The value that should be taken as the target for the chemical bond associated with the specified atoms, expressed as a bond order.
pdbx_ordinal	integer	Ordinal index for the component bond list.
pdbx_stereo_config	text	Stereochemical configuration across a double bond.
pdbx_aromatic_flag	text	A flag indicating an aromatic bond.

pdbx_chem_comp_descriptor

Column	Type	Description
prd_id	text	PRDID of an entry. All tables/categories refer back to the PRDID in the brief_summary table.
comp_id	text	This data item is a pointer to _chem_comp.id in the CHEM_COMP category.
descriptor	text	This data item contains the descriptor value for this component.
type	text	This data item contains the descriptor type.
program	text	This data item contains the name of the program or library used to compute the descriptor.
program_version	text	This data item contains the version of the program or library used to compute the descriptor.

pdbx_chem_comp_identifier

Column	Type	Description
prd_id	text	PRDID of an entry. All tables/categories refer back to the PRDID in the brief_summary table.
comp_id	text	This data item is a pointer to _chem_comp.id in the CHEM_COMP category.
identifier	text	This data item contains the identifier value for this component.
type	text	This data item contains the identifier type.
program	text	This data item contains the name of the program or library used to compute the identifier.
program_version	text	This data item contains the version of the program or library used to compute the identifier.

pdbx_prd_audit

Column	Type	Description
prd_id	text	PRDID of an entry. All tables/categories refer back to the PRDID in the brief_summary table.
date	date	The date associated with this audit record.
processing_site	text	An identifier for the wwPDB site creating or modifying the molecule.
action_type	text	The action associated with this audit record.

pdbx_reference_entity_link

Column	Type	Description
prd_id	text	PRDID of an entry. All tables/categories refer back to the PRDID in the brief_summary table.
link_id	integer	The value of _pdbx_reference_entity_link.link_id uniquely identifies linkages between entities with a molecule.
ref_entity_id_1	text	The reference entity id of the first of the two entities joined by the linkage. This data item is a pointer to _pdbx_reference_entity_list.ref_entity_id in the PDBX_REFERENCE_ENTITY_LIST category.
ref_entity_id_2	text	The reference entity id of the second of the two entities joined by the linkage. This data item is a pointer to _pdbx_reference_entity_list.ref_entity_id in the PDBX_REFERENCE_ENTITY_LIST category.
entity_seq_num_1	integer	For a polymer entity, the sequence number in the first of the two entities containing the linkage. This data item is a pointer to _pdbx_reference_entity_poly_seq.num in the PDBX_REFERENCE_ENTITY_POLY_SEQ category.
entity_seq_num_2	integer	For a polymer entity, the sequence number in the second of the two entities containing the linkage. This data item is a pointer to _pdbx_reference_entity_poly_seq.num in the PDBX_REFERENCE_ENTITY_POLY_SEQ category.
comp_id_1	text	The component identifier in the first of the two entities containing the linkage. For polymer entities, this data item is a pointer to _pdbx_reference_entity_poly_seq.mon_id in the PDBX_REFERENCE_ENTITY_POLY_SEQ category. For non-polymer entities, this data item is a pointer to _pdbx_reference_entity_nonpoly.chem_comp_id in the PDBX_REFERENCE_ENTITY_NONPOLY category.
comp_id_2	text	The component identifier in the second of the two entities containing the linkage. For polymer entities, this data item is a pointer to _pdbx_reference_entity_poly_seq.mon_id in the PDBX_REFERENCE_ENTITY_POLY_SEQ category. For non-polymer entities, this data item is a pointer to _pdbx_reference_entity_nonpoly.chem_comp_id in the PDBX_REFERENCE_ENTITY_NONPOLY category.
atom_id_1	text	The atom identifier/name in the first of the two entities containing the linkage.
atom_id_2	text	The atom identifier/name in the second of the two entities containing the linkage.
value_order	text	The bond order target for the chemical linkage.
component_1	integer	The entity component identifier for the first of two entities containing the linkage.
component_2	integer	The entity component identifier for the second of two entities containing the linkage.
link_class	text	A code indicating the entity types involved in the linkage.

pdbx_reference_entity_list

Column	Type	Description
prd_id	text	PRDID of an entry. All tables/categories refer back to the PRDID in the brief_summary table.
ref_entity_id	text	The value of _pdbx_reference_entity_list.ref_entity_id is a unique identifier the a constituent entity within this reference molecule.
type	text	Defines the polymer characteristic of the entity.
details	text	Additional details about this entity.
component_id	integer	The component number of this entity within the molecule.

pdbx_reference_entity_nonpoly

Column	Type	Description
prd_id	text	PRDID of an entry. All tables/categories refer back to the PRDID in the brief_summary table.
ref_entity_id	text	The value of _pdbx_reference_entity_nonpoly.ref_entity_id is a reference to _pdbx_reference_entity_list.ref_entity_id in PDBX_REFERENCE_ENTITY_LIST category.
name	text	A name of the non-polymer entity.
chem_comp_id	text	For non-polymer entities, the identifier corresponding to the chemical definition for the molecule.

pdbx_reference_entity_poly

Column	Type	Description
prd_id	text	PRDID of an entry. All tables/categories refer back to the PRDID in the brief_summary table.
ref_entity_id	text	The value of _pdbx_reference_entity_poly.ref_entity_id is a reference to _pdbx_reference_entity_list.ref_entity_id in PDBX_REFERENCE_ENTITY_LIST category.
type	text	The type of the polymer.
db_code	text	The database code for this source information
db_name	text	The database name for this source information

pdbx_reference_entity_poly_link

Column	Type	Description
prd_id	text	PRDID of an entry. All tables/categories refer back to the PRDID in the brief_summary table.
link_id	integer	The value of _pdbx_reference_entity_poly_link.link_id uniquely identifies a linkage within a polymer entity.
ref_entity_id	text	The reference entity id of the polymer entity containing the linkage. This data item is a pointer to _pdbx_reference_entity_poly.ref_entity_id in the PDBX_REFERENCE_ENTITY_POLY category.
component_id	integer	The entity component identifier entity containing the linkage.
entity_seq_num_1	integer	For a polymer entity, the sequence number in the first of the two components making the linkage. This data item is a pointer to _pdbx_reference_entity_poly_seq.num in the PDBX_REFERENCE_ENTITY_POLY_SEQ category.
entity_seq_num_2	integer	For a polymer entity, the sequence number in the second of the two components making the linkage. This data item is a pointer to _pdbx_reference_entity_poly_seq.num in the PDBX_REFERENCE_ENTITY_POLY_SEQ category.
comp_id_1	text	The component identifier in the first of the two components making the linkage. This data item is a pointer to _pdbx_reference_entity_poly_seq.mon_id in the PDBX_REFERENCE_ENTITY_POLY_SEQ category.
comp_id_2	text	The component identifier in the second of the two components making the linkage. This data item is a pointer to _pdbx_reference_entity_poly_seq.mon_id in the PDBX_REFERENCE_ENTITY_POLY_SEQ category.
atom_id_1	text	The atom identifier/name in the first of the two components making the linkage.
atom_id_2	text	The atom identifier/name in the second of the two components making the linkage.
value_order	text	The bond order target for the non-standard linkage.

pdbx_reference_entity_poly_seq

Column	Type	Description
prd_id	text	PRDID of an entry. All tables/categories refer back to the PRDID in the brief_summary table.
ref_entity_id	text	The value of _pdbx_reference_entity_poly_seq.ref_entity_id is a reference to _pdbx_reference_entity_poly.ref_entity_id in PDBX_REFERENCE_ENTITY_POLY category.
mon_id	text	This data item is the chemical component identifier of monomer.
parent_mon_id	text	This data item is the chemical component identifier for the parent component corresponding to this monomer.
num	integer	The value of _pdbx_reference_entity_poly_seq.num must uniquely and sequentially identify a record in the PDBX_REFERENCE_ENTITY_POLY_SEQ list. This value is conforms to author numbering conventions and does not map directly to the numbering conventions used for _entity_poly_seq.num.
observed	text	A flag to indicate that this monomer is observed in the instance example.
hetero	text	A flag to indicate that sequence heterogeneity at this monomer position.

pdbx_reference_entity_sequence

Column	Type	Description
prd_id	text	PRDID of an entry. All tables/categories refer back to the PRDID in the brief_summary table.
ref_entity_id	text	The value of _pdbx_reference_entity_sequence.ref_entity_id is a reference to _pdbx_reference_entity_list.ref_entity_id in PDBX_REFERENCE_ENTITY_LIST category.
type	text	The monomer type for the sequence.
NRP_flag	text	A flag to indicate a non-ribosomal entity.

pdbx_reference_entity_src_nat

Column	Type	Description
prd_id	text	PRDID of an entry. All tables/categories refer back to the PRDID in the brief_summary table.
ref_entity_id	text	The value of _pdbx_reference_entity_src_nat.ref_entity_id is a reference to _pdbx_reference_entity_list.ref_entity_id in PDBX_REFERENCE_ENTITY_LIST category.
ordinal	integer	The value of _pdbx_reference_entity_src_nat.ordinal distinguishes source details for this entity.
organism_scientific	text	The scientific name of the organism from which the entity was isolated.
strain	text	The strain of the organism from which the entity was isolated.
taxid	text	The NCBI TaxId of the organism from which the entity was isolated.
db_code	text	The database code for this source information
db_name	text	The database name for this source information
source	text	The data source for this information.

pdbx_reference_entity_subcomponents

Column	Type	Description
prd_id	text	PRDID of an entry. All tables/categories refer back to the PRDID in the brief_summary table.
seq	text	The subcomponent sequence for the entity.
chem_comp_id	text	For entities represented as single molecules, the identifier corresponding to the chemical definition for the molecule.

pdbx_reference_molecule

Column	Type	Description
prd_id	text	PRDID of an entry. All tables/categories refer back to the PRDID in the brief_summary table.
formula_weight	double precision	Formula mass in daltons of the entity.
formula	text	The formula for the reference entity. Formulae are written according to the rules: 1. Only recognised element symbols may be used. 2. Each element symbol is followed by a 'count' number. A count of '1' may be omitted. 3. A space or parenthesis must separate each element symbol and its count, but in general parentheses are not used. 4. The order of elements depends on whether or not carbon is present. If carbon is present, the order should be: C, then H, then the other elements in alphabetical order of their symbol. If carbon is not present, the elements are listed purely in alphabetic order of their symbol. This is the 'Hill' system used by Chemical Abstracts.
type	text	Defines the structural classification of the entity.
type_evidence_code	text	Evidence for the assignment of _pdbx_reference_molecule.type
class	text	Broadly defines the function of the entity.
class_evidence_code	text	Evidence for the assignment of _pdbx_reference_molecule.class
name	text	A name of the entity.
represent_as	text	Defines how this entity is represented in PDB data files.
chem_comp_id	text	For entities represented as single molecules, the identifier corresponding to the chemical definition for the molecule.
compound_details	text	Special details about this molecule.
description	text	Description of this molecule.
representative_PDB_id_code	text	The PDB accession code for the entry containing a representative example of this molecule.
release_status	text	Defines the current PDB release status for this molecule definition.
replaces	text	Assigns the identifier for the reference molecule which have been replaced by this reference molecule. Multiple molecule identifier codes should be separated by commas.
replaced_by	text	Assigns the identifier of the reference molecule that has replaced this molecule.