wwPDB: Chemical Component Dictionary

wwPDB: Chemical Component Dictionary
Data Dictionaries
PDBx/mmCIF
Chemical Component Dictionary
Biologically Interesting Molecule Reference Dictionary (BIRD)
Chemical Component Dictionary
The Chemical Component Dictionary is as an external reference file describing all residue and small molecule components found in PDB entries. This dictionary contains detailed chemical descriptions for standard and modified amino acids/nucleotides, small molecule ligands, and solvent molecules. Each chemical definition includes descriptions of chemical properties such as stereochemical assignments, chemical descriptors (SMILES & InChI), systematic chemical names, and idealized coordinates (generated using Molecular Networks' Corina, and if there are issues, OpenEye's OMEGA).
The dictionary is organized by the 3-character alphanumeric code that PDB assigns to each chemical component. New chemical component definitions appear in the dictionary as the entries in which they are observed are released in the PDB archive; consequently, the dictionary is updated with each weekly PDB release. The dictionary is regularly reviewed and remediated. Any obsoleted components remain in the dictionary marked with status OBS.
Users can search and browse the Chemical Component Dictionary using resources such as
PDBeChem
and
RCSB PDB Chemical Search.
The entire Chemical Component Dictionary and the companion dictionary of amino acid protonation variants can be downloaded from the wwPDB ftp site:
Chemical Component Dictionary:
mmCIF (gz)
SDF/MOL (gz)
Protonation Variants Companion Dictionary:
mmCIF (gz)
Chemical Component Model data file:
mmCIF (gz)
In addition, SMILES/InChI/InChIKey data files can be downloaded here:
SMILES (OpenEye with stereo) (
tab delimited text
SMILES (OpenEye) (
tab delimited text
SMILES (CACTVS with stereo) (
tab delimited text
SMILES (CACTVS) (
tab delimited text
InChI (
tab delimited text
InChIKey (
tab delimited text
Please note that these files are large, and may take a while to download. You may wish to right-click on the "plain text" link to save the file.
The dictionary of protonation variants provides additional nomenclature information for the protonation states of standard amino acids in N-terminal, C-terminal, and free forms, and includes common side chain protonation states. The identifiers used in this extension dictionary longer identifier codes to distinguish the various protonation forms of the standard amino acids. For instance, an identifier code
ARG_LFOH_DHH12
is used to identify the arginine variant with a neutral peptide unit and side chain protonated at NH1. The extended identifier codes are not compatible with the 3-character format restrictions for the residue identifier in the PDB format, so these codes do not currently appear in PDB files. In PDB entries, protonated residues are identified by the 3-character code of their parent amino acid; however, the atom nomenclature for protonated forms will be taken from the variant dictionary definitions.
The
Chemical Component Model data file
contains the matching chemical structures in the Chemical Component Dictionary and the Cambridge Structural Database (CSD) archive. This reference file includes accession code correspondences, Cartesian coordinates and R-value, data-collection temperature and a disorder flag, SMILES and InChI descriptors, and a Digital Object Identifier (DOI) for the citation associated with the CSD entry.
Prior to development of the Chemical Component Dictionary, PDB chemical information was solely in the form of connection tables. This older representation, called the PDB HET dictionary, is still made available on the wwPDB ftp site (
). PDB HET format dictionary entries for individual components are available at
The Chemical Component Dictionary was formerly called the HET Group Dictionary.
Descriptions of chemical components in
mmCIF
and
PDB
formats are provided below.
J.D. Westbrook, C. Shao, Z. Feng, M. Zhuravleva, S. Velankar, J. Young (2014) The chemical component dictionary: complete descriptions of constituent molecules in experimentally determined 3D macromolecules in the Protein Data Bank Bioinformatics doi:
10.1093/bioinformatics/btu789
PDBeChem
PDBeChem
offers a wide range of possibilities for searching and exploring the dictionary:
Search for a particular 3-letter code
Search using part of the name
Search for a formula range
Search for a substructure
Search for a fragment expression
Users can also search by references in macromolecules, molecule classification, and atom energy type.
A generic browsing interface lets users follow links that are available from every record in order to navigate through the relationships of the dictionary. For example, a relationship link can be followed to view the atoms of a ligand and then for a particular atom, its bonds and energy types and so on.
For more information, please see
RCSB PDB Chemical Search
RCSB PDB
Chemical Search
can be used to navigate the Chemical Component Dictionary.
The
Chemical Similarity
search allows you to find small molecules in the PDB archive that are similar to your query. These molecules are found in the
Chemical Component Dictionary (CCD)
and the
Biologically Interesting Molecule Reference Dictionary (BIRD)
. You can search using properties such as
molecular formula
or
chemical descriptors
You can use this search to find chemical components (for example, drugs, inhibitors, modified residues, or building blocks such as amino acids and nucleotides) that:
are
similar
to the query formula or descriptor (e.g., differing by one or two atoms or functional groups),
contain
the query formula or descriptor as a substructure within a larger molecule, or
exactly or very closely match
the query formula or descriptor.
Chemical Components in mmCIF Format
The mmCIF format combines collections of related data items (tokens) into categories. A category is essentially a table in which each token represents a row in the table. The question mark (?) is used to mark an item value as missing. A period (.) may be used to identify that there is no appropriate value for the item or that a value has been intentionally omitted.
Vectors and tables of data may be encoded in mmCIF using a loop_ directive. To build a table, the data item names corresponding to the table columns are preceded by the loop_ directive, and followed by the corresponding rows of data.
A detailed description of the
mmCIF
syntax and logic structure is available.
In the Chemical Component Dictionary, each chemical component is defined by sets of tokens in the five categories. Click on a category link to see the dictionary definitions of the category contents (with examples).
chem_comp
Token
Definition
Example
_chem_comp.id
The alphanumeric code for the chemical component.
HYP
_chem_comp.name
The name of the chemical component.
4-HYDROXYPROLINE
_chem_comp.type
The type of monomer.
L-peptide linking
_chem_comp.pdbx_type
A preliminary internal classification used by PDB.
ATOMP
_chem_comp.formula
The chemical formula of the chemical component.
C5 H9 N1 O3'
_chem_comp.mon_nstd_parent_comp_id
The identifier for the parent component of the nonstandard component. May be a comma-separated list if this component is derived from multiple components.
PRO
_chem_comp.pdbx_synonyms
Synonym list for the non-standard residue.
HYDROXYPROLINE
_chem_comp.pdbx_formal_charge
The formal charge on the chemical component.
+1
_chem_comp.pdbx_initial_date
Date the chemical component was added to the database.
yyyy-mm-dd
_chem_comp.pdbx_modified_date
Date that the component was last modified.
yyyy-mm-dd
_chem_comp.pdbx_ambiguous_flag
For ligands with unconventional bonding (i.e. ligands with transition metal complexes).
code
_chem_comp.pdbx_release status
Status of ligand (released, hold, obsoleted).
yyyy-mm-dd
_chem_comp.pdbx_replaced_by
Identifies the _chem_comp.id of the new component that has replaced this component.
3-letter identifier
_chem_comp.pdbx_replaces
Identifies the _chem_comp.id of the component this entry replaces. Converse of _replaced_by.
3-letter identifier
_chem_comp.formula_weight
Formula mass of the chemical component in Daltons.
131.131
_chem_comp.one_letter_code
Reports the one-letter code of the component, if applicable.
one-letter identifier
_chem_comp.three_letter_code
Reports the three-letter code of the component, if applicable.
ATP
_chem_comp.pdbx_model_coordinates_details
Provides additional details about the model coordinates in the component definition.
text
_chem_comp.pdbx_model_coordinates_missing_flag
This data item identifies if model coordinates are missing in this definition
Y or N
_chem_comp.pdbx_ideal_coordinates_details
Identifies the source of the ideal coordinates in the component definition.
text
_chem_comp.pdbx_ideal_coordinates_missing_flag
Identifies if ideal coordinates are missing in this definition.
Y or N
_chem_comp.pdbx_model_coordinates_db_code
Identifies the PDB database code from which the heavy atom model coordinates were obtained.
PDB entry id
_chem_comp.pdbx_processing_site
Identifies the deposition site that processed this chemical component defintion.
RCSB PDB, PDBj, PDBe
chem_comp_atom
Tokens in this section are looped through for each atom in the chemical component
Token
Definition
Example
_chem_comp_atom.comp_id
Same as _chem_comp.id
HYP
_chem_comp_atom.atom_id
Identifier for each atom in the chemical component - new format
CA
_chem_comp_atom.alt_atom_id
Previous format of identifier for each atom in the chemical component.
CA
_chem_comp_atom.type_symbol
The element type for each atom in the chemical component.
C O N, etc.
_chem_comp_atom.charge
The formal charge assigned to each atom in the chemical component.
_chem_comp_atom.pdbx_align
Determines which column the atom name appears within the PDB coordinate files. The possible values are 0 or 1.
0 or 1
_chem_comp_atom.pdbx_aromatic_flag
Defines atoms in an aromatic moiety.
Y or N
_chem_comp_atom.pdbx_leaving_atom_flag
Flags atoms with "leaving" capability.
Y or N
_chem_comp_atom.pdbx_stereo_config
Defines the stereochemical configuration of the chiral center atom.
R or S or N
_chem_comp_atom.model_Cartn_x
The x component of the coordinates for each atom specified as orthogonal angstroms.
26.056
_chem_comp_atom.model_Cartn_y
The y component of the coordinates for each atom specified as orthogonal angstroms.
5.609
_chem_comp_atom.model_Cartn_z
The z component of the coordinates for each atom specified as orthogonal angstroms.
5.594
_chem_comp_atom.pdbx_model_Cartn_x_ideal
Computed idealized coordinates, x component of the vector (in Angstroms)
number
_chem_comp_atom.pdbx_model_Cartn_y_ideal
Computed idealized coordinates, y component of the vector (in Angstroms)
number
_chem_comp_atom.pdbx_model_Cartn_z_ideal
Computed idealized coordinates, z component of the vector (in Angstroms)
number
_chem_comp_atom.pdbx_ordinal
Ordinal index for the chemical component atom list.
1 (integer)
chem_comp_bond
Tokens in this section are looped through for each bond in the chemical component
Token
Definition
Example
_chem_comp_bond.comp_id
Same as _chem_comp.id
HYP
_chem_comp_bond.atom_id_1
The ID of the first of the two atoms that define the bond.
chem_comp_bond.atom_id_2
The ID of the second of the two atoms that define the bond.
CA
_chem_comp_bond.value_order
The bond order of the chemical bond associated with the specified atoms.
SING
_chem_comp_bond.pdbx_aromatic_flag
Defines aromatic bonds.
Y or N
_chem_comp_bond.pdbx_stereo_config
Defines stereochemical bonds.
Y or N
_chem_comp_bond.pdbx_ordinal
Ordinal index for the component bond list.
1 (integer)
pdbx_chem_comp_descriptor
Token
Definition
Example
_pdbx_chem_comp_descriptor.comp_id
This data item is a pointer to _chem_comp.id in the CHEM_COMP category.
text
_pdbx_chem_comp_descriptor.type
The type of the program or library used to compute the descriptor.
text
_pdbx_chem_comp_descriptor.program
The name of the program or library used to compute the descriptor.
text
_pdbx_chem_comp_descriptor.program_version
The version of the program or library used to compute the descriptor.
version number
_pdbx_chem_comp_descriptor.descriptor
The chemical descriptor value for this component.
code
pdbx_chem_comp_identifier
Token
Definition
Example
_pdbx_chem_comp_identifier.comp_id
This data item is a pointer to _chem_comp.id in the CHEM_COMP category.
text
_pdbx_chem_comp_identifier.type
Contains the identifier type.
CAS Reg No. or PUBCHEM, etc.
_pdbx_chem_comp_identifier.program
The name of the program or library used to compute the identifier.
OpenEye OECHEM program, etc.
_pdbx_chem_comp_identifier.program_version
The version of the program or library used to compute the identifier.
v1.2 (numbers)
_pdbx_chem_comp_identifier.identifier
Contains the identifier value for this chemical component..
text
In a PDB entry, the mmCIF category chem_comp is used to describe the chemical components in the file. The chemical name is described in chem_comp.name, chemical formula in chem_comp.formula, and molecular weight in chem_comp.formula_weight.
For example, the mmCIF file for PDB entry 1t5d contains the ligand 4-Chloro-benzoic Acid (ID code: 174):
data_174
_chem_comp.id 174
_chem_comp.name "4-CHLORO-BENZOIC ACID"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C7 H5 Cl O2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2004-05-07
_chem_comp.pdbx_modified_date 2008-04-29
_chem_comp.pdbx_ambiguous_flag N
_chem_comp.pdbx_release_status REL
_chem_comp.pdbx_replaced_by ?
_chem_comp.pdbx_replaces ?
_chem_comp.formula_weight 156.566
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 174
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details ?
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code  1T5D
_chem_comp.pdbx_processing_site RCSB
Further information describing this residue (174) is then provided in the Chemical Component Dictionary (See the
example
below).
Chemical Components in PDB Format
The heterogen section of a PDB coordinate file describes ligands in the entry. The chemical name of the ligand is given in the HETNAM record and the chemical formula is given in the FORMUL record. Any synonyms for the chemical name are given in the HETSYN records.
For example, the PDB format file for PDB entry 1t5d contains the ligand 4-Chloro-benzoic Acid (ID code: 174):
HET 174 15
HETNAM 174 4-CHLORO-BENZOIC ACID
FORMUL 174 C7 H5 CL O2
Further information describing this residue (174) is then provided in the Chemical Component Dictionary (See the
example
below).
Please refer to the
PDB File Format Guide
for further description.
Examples
Chemical Component Dictionary (mmCIF Format)
data_174
_chem_comp.id 174
_chem_comp.name "4-CHLORO-BENZOIC ACID"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C7 H5 Cl O2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2004-05-07
_chem_comp.pdbx_modified_date 2008-04-29
_chem_comp.pdbx_ambiguous_flag N
_chem_comp.pdbx_release_status REL
_chem_comp.pdbx_replaced_by ?
_chem_comp.pdbx_replaces ?
_chem_comp.formula_weight 156.566
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 174
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details ?
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 1T5D
_chem_comp.pdbx_processing_site RCSB
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.alt_atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.charge
_chem_comp_atom.pdbx_align
_chem_comp_atom.pdbx_aromatic_flag
_chem_comp_atom.pdbx_leaving_atom_flag
_chem_comp_atom.pdbx_stereo_config
_chem_comp_atom.model_Cartn_x
_chem_comp_atom.model_Cartn_y
_chem_comp_atom.model_Cartn_z
_chem_comp_atom.pdbx_model_Cartn_x_ideal
_chem_comp_atom.pdbx_model_Cartn_y_ideal
_chem_comp_atom.pdbx_model_Cartn_z_ideal
_chem_comp_atom.pdbx_ordinal
174 CL4 CL4 CL 0 0 N N N -19.787 95.862 18.541 0.032 -0.000 -3.376 1
174 C4 C4 C 0 1 Y N N -19.932 94.201 19.219 0.005 -0.000 -1.640 2
174 C5 C5 C 0 1 Y N N -18.817 93.715 19.901 -1.205 0.000 -0.969 3
174 C6 C6 C 0 1 Y N N -18.847 92.452 20.466 -1.233 0.000 0.409 4
174 C3 C3 C 0 1 Y N N -21.099 93.428 19.089 1.196 -0.000 -0.932 5
174 C2 C2 C 0 1 Y N N -21.127 92.158 19.664 1.182 0.004 0.446 6
174 C1 C1 C 0 1 Y N N -19.996 91.681 20.342 -0.036 -0.000 1.128 7
174 C C C 0 1 N N N -19.962 90.330 20.989 -0.059 -0.000 2.605 8
174 O1 O1 O 0 1 N N N -20.968 89.592 20.924 1.097 -0.001 3.296 9
174 O2 O2 O 0 1 N N N -18.919 89.991 21.597 -1.120 0.000 3.196 10
174 H5 H5 H 0 1 N N N -17.907 94.332 19.994 -2.130 0.001 -1.526 11
174 H6 H6 H 0 1 N N N -17.967 92.065 21.008 -2.178 0.000 0.931 12
174 H3 H3 H 0 1 N N N -21.978 93.812 18.545 2.138 -0.001 -1.461 13
174 H2 H2 H 0 1 N N N -22.035 91.537 19.583 2.110 0.003 0.997 14
174 HO1 HO1 H 0 1 N N N -20.946 88.735 21.334 1.082 -0.001 4.263 15
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_aromatic_flag
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_ordinal
174 CL4 C4 SING N N 1
174 C4 C5 DOUB Y N 2
174 C4 C3 SING Y N 3
174 C5 C6 SING Y N 4
174 C5 H5 SING N N 5
174 C6 C1 DOUB Y N 6
174 C6 H6 SING N N 7
174 C3 C2 DOUB Y N 8
174 C3 H3 SING N N 9
174 C2 C1 SING Y N 10
174 C2 H2 SING N N 11
174 C1 C SING N N 12
174 C O1 SING N N 13
174 C O2 DOUB N N 14
174 O1 HO1 SING N N 15
loop_
_pdbx_chem_comp_descriptor.comp_id
_pdbx_chem_comp_descriptor.type
_pdbx_chem_comp_descriptor.program
_pdbx_chem_comp_descriptor.program_version
_pdbx_chem_comp_descriptor.descriptor
174 SMILES ACDLabs 10.04 O=C(O)c1ccc(Cl)cc1
174 SMILES_CANONICAL CACTVS 3.341 OC(=O)c1ccc(Cl)cc1
174 SMILES CACTVS 3.341 OC(=O)c1ccc(Cl)cc1
174 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 c1cc(ccc1C(=O)O)Cl
174 SMILES "OpenEye OEToolkits" 1.5.0 c1cc(ccc1C(=O)O)Cl
174 InChI InChI 1.02b InChI=1/C7H5ClO2/c8-6-
3-1-5(2-4-6)7(9)10/h1-4H,(H,9,10)/f/h9H
174 InChIKey InChI 1.02b XRHGYUZYPHTUJZ-BGGKNDAXCA
loop_
_pdbx_chem_comp_identifier.comp_id
_pdbx_chem_comp_identifier.type
_pdbx_chem_comp_identifier.program
_pdbx_chem_comp_identifier.program_version
_pdbx_chem_comp_identifier.identifier
174 "SYSTEMATIC NAME" ACDLabs 10.04 "4-chlorobenzoic acid"
174 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "4-chlorobenzoic acid"
Heterogen List (PDB Format)
RESIDUE 174 15
CONECT CL4 1 C4
CONECT C4 3 CL4 C5 C3
CONECT C5 3 C4 C6 H5
CONECT C6 3 C5 C1 H6
CONECT C3 3 C4 C2 H3
CONECT C2 3 C3 C1 H2
CONECT C1 3 C6 C2 C
CONECT C 3 C1 O1 O2
CONECT O1 2 C HO1
CONECT O2 1 C
CONECT H5 1 C5
CONECT H6 1 C6
CONECT H3 1 C3
CONECT H2 1 C2
CONECT HO1 1 O1
END
HET 174 15
HETNAM 174 4-CHLORO-BENZOIC ACID
FORMUL 174 7 H5 Cl1 O2
D. Dimitropoulos, J. Ionides, K. Henrick (2006) UNIT 14.3: Using MSDchem to search the PDB ligand dictionary In Current Protocols in Bioinformatics (A.D. Baxevanis, R.D.M. Page, G.A. Petsko, L.D. Stein, and G.D. Stormo, eds.) pp 14.3.1-14.3.3 John Wiley & Sons, Hoboken, NJ.
Z. Feng, L. Chen, H. Maddula, O. Akcan, R. Oughtred, H.M. Berman, J. Westbrook. (2004) Ligand Depot: a data warehouse for ligands bound to macromolecules. Bioinformatics 20(13):2153-2155.