PDB Chemical Component Dictionary Format Description

The PDB Chemical Component Dictionary (formerly the HET Group Dictionary) is available in mmCIF format [68.7 Mb uncompressed or 15.97 Mb .gz format], and is updated weekly. This dictionary, created by the curation efforts of the RCSB PDB team, is under active development. Any comments and suggestions are greatly appreciated.

This page provides descriptions and examples of the contents of the PDB format and mmCIF format Chemical Component Dictionaries as well as a description of the contents of a Ligand Expo entry.

Ligand Expo¹, formally the Ligand Depot, has been created as a data warehouse which integrates databases, services, tools and methods related to small molecules bound to macromolecules. Its purpose is to help users explore the PDB Chemical Component Dictionary and the small molecule contents of the PDB. In particular, it allows users to:

• Search for chemical components by chemical name, formula, or chemical description
• Search for chemical components by 3-letter ID
• Find a chemical components by structure or substructure

Introduction

The mmCIF format [~16 Mb] Chemical Component Dictionaries describe all residues in the PDB, both standard and non-standard, in addition to all the small molecule ligands. The overall format of the dictionaries is an alphabetical concatenation of all available groups.

Ligands are identified in the mmCIF format files as chemical components and PDB format files as HET groups. Residues such as prosthetic groups, inhibitors, solvent molecules, and ions for which coordinates are supplied are considered to be non-standard if they are:

• not one of the standard amino acids, and
  
• not one of the nucleic acids (C/dC, G/dG, A/dA, dT, U/dU, and I/dI), and
  
• an unknown amino acid or nucleic acid where UNK is used to indicate the unknown residue name.
  

Each chemical component is assigned an ID code of not more than three alphanumeric characters.

Each time a new chemical component is created, it is entered into both the mmCIF format and PDB format dictionaries. A new group is not released in the public version of the dictionary until the PDB entry containing the novel chemical component is released.

Table of Contents

• mmCIF Format
• Dictionary Record Format
• Example: 4-Chloro-benzoic Acid
• Ligand Expo
• PDB Format
• Dictionary Record Format
• Example: 4-Chloro-benzoic Acid
• Additional Resources
• Reference

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.

In an mmCIF format coordinate file the chem_comp category is used to describe the chemical components in an entry. The chemical name for the chemical component is given by chem_comp.name, the chemical formula by chem_comp.formula, and the molecular weight by chem_comp.formula_weight.

For example entry 1t5d contains the ligand 4-Chloro-benzoic Acid (ID code: 174):

loop_
_chem_comp.id
_chem_comp.name
_chem_comp.ndb_synonyms
_chem_comp.formula
_chem_comp.formula_weight
_chem_comp.ndb_component_no
174 '4-CHLORO-BENZOIC ACID' ? 'C7 H5 O2 CL1'    156.568 ?
#

Further information describing each non-standard residue is then provided in the Chemical Component Dictionary.

Dictionary Record Format

In the mmCIF format Chemical Component Dictionary, each chemical component is defined by sets of tokens in the five categories: chem_comp (Table 1), chem_comp_atom (Table 2), chem_comp_bond (Table 3), pdbx_chem_comp_descriptor (Table 4), and pdbx_chem_comp_identifier (Table 5).

HYP

4-HYDROXYPROLINE

L-peptide linking

ATOMP

C5 H9 N1 O3'

PRO

HYDROXYPROLINE

+1

yyyy-mm-dd

yyyy-mm-dd

code

yyyy-mm-dd

3-letter identifier

3-letter identifier

131.131

one-letter identifier

ATP

text

Y or N

text

Y or N

PDB entry id

RCSB PDB, PDBj, PDBe

HYP

CA

CA

C  O  N, etc.

0

0 or 1

Y or N

Y or N

R or S or N

26.056

5.609 

5.594

number

number

number

1 (integer)

HYP

N 

CA

SING 

Y or N

Y or N

1 (integer)

text

text

text

version number

code

text

CAS Reg No. or PUBCHEM, etc.

OpenEye OECHEM program, etc.

v1.2 (numbers)

text

Example: 4-Chloro-benzoic Acid

Diagram of 4-Chloro-benzoic Acid

data_ACY
# 
_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 O2 CL1'
_chem_comp.mon_nstd_flag    n 

_chem_comp.formula_weight   156.568
# 
loop_
_chem_comp_atom.comp_id 
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol 
_chem_comp_atom.charge 
_chem_comp_atom.model_Cartn_x
_chem_comp_atom.model_Cartn_y 
_chem_comp_atom.model_Cartn_z 

_chem_comp_atom.pdbx_align 
174 CL4 CL 0 -19.787 95.862 18.541 0 
174 C4  C  0 -19.932 94.201 19.219 1 
174 C5  C  0 -18.817 93.715 19.901 1 
174 C6  C  0 -18.847 92.452 20.466 1 
174 C3  C  0 -21.099 93.428 19.089 1 
174 C2  C  0 -21.127 92.158 19.664 1 
174 C1  C  0 -19.996 91.681 20.342 1 
174 C   C  0 -19.962 90.330 20.989 1 
174 O1  O  0 -20.968 89.592 20.924 1 
174 O2  O  0 -18.919 89.991 21.597 1 
174 HO1 H  0 ?       ?      ?      1 
174 H2  H  0 ?       ?      ?      1 
174 H3  H  0 ?       ?      ?      1 
174 H5  H  0 ?       ?      ?      1 
174 H6  H  0 ?       ?      ?      1 
# 
loop_
_chem_comp_bond.comp_id 
_chem_comp_bond.atom_id_1 
_chem_comp_bond.atom_id_2 
_chem_comp_bond.value_order 
174 CL4 C4  SING 
174 C4  C5  AROM 
174 C4  C3  AROM 
174 C5  C6  AROM 
174 C5  H5  SING 
174 C6  C1  AROM 
174 C6  H6  SING 
174 C3  C2  AROM 
174 C3  H3  SING 
174 C2  C1  AROM 
174 C2  H2  SING 
174 C1  C   SING 
174 C   O1  SING 
174 C   O2  DOUB 
174 O1  HO1 SING 
# 

PDB Format

We also have the Heterogen List available for download [13.2 Mb]. However, the RCSB PDB recommends use of the mmCIF format chemical component dictionary because the heterogen list does not take stereochemistry into account, among other chemical properties, making this ligand library more limited in its functionality. But many still find it a useful tool.

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 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 O2 CL1

Further information describing each non-standard residue is then provided in the Chemical Component Dictionary.

Dictionary Record Format

Each entry in the PDB format Chemical Component Dictionary is represented by a series of fields:

HYP 18

N 3 CA CD H

HYP 18

HYP HYDROXYPROLINE

HYP 4-HYDROXYPROLINE

HYP    C5 H9 N1 O3

Example: 4-Chloro-benzoic Acid

Diagram of 4-Chloro-benzoic Acid

RESIDUE   174     15
CONECT     CL4     1 C4  
CONECT      C4     3CL4   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      HO1    1 O1  
CONECT      H2     1 C2  
CONECT      H3     1 C3  
CONECT      H5     1 C5  
CONECT      H6     1 C6  
END
HET    174             15
HETNAM     174 4-CHLORO-BENZOIC ACID
FORMUL      174    C7 H5 O2 CL1

Name of the chemical component
Formula of the chemical component
Link to the mmCIF format Chemical Component Dictionary for the chemical component
JAVA applet image of the chemical component
A link to a drawing tool where the chemical component can be modified graphically
A listing of all of the PDB entries in which the chemical component is found
A table with links to download the coordinates (PDB, mmCIF and mol2 formats) of the chemical component in each of the PDB entries in which it is found