university lille north of france LigASite database of binding sites

PDB ID and HEADER, TITLE and COMPND records of the PDB file.

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Illustration of Binding SiteHelp

Figure showing the binding site residues. Ligands are displayed as CPK. Figures were drawn with Molscript (7) and rendered with Raster3D (8). PISA coordinates (3) are used when available (all entries except NMR). Ligands do not appear on the picture when PISA fails to apply symmetry operations to ligand coordinates.

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HETgroup - Residue ContactsHelp

List of binding site residues detected in this holo-structure.

Column 1 gives the position, coloured on a yellow-to-red scale depending on the number of holo-structures where the residue is in contact with a ligand.
Column 2 gives the identifier of the chain to which the residue belongs.
Column 3 gives the 3-letter amino acid code, coloured according to physico-chemical type.

The binding residues in this holo structure are listed for each ligand independently, following the ligand's unique ID.

Note that since PISA files are used whenever available, chain identifiers may differ from those in original PDB files.

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EDR D 999
117C GLY
118C GLY
119C GLY
121C TYR
122C SER
127C LEU
130C TYR
199C GLU
200C SER
233C TRP
288C PHE
290C PHE
330C PHE
331C PHE
440C HIS
441C GLY
442C TYR
444C ILE
EDR B 999
117A GLY
118A GLY
119A GLY
121A TYR
122A SER
130A TYR
199A GLU
200A SER
233A TRP
288A PHE
290A PHE
330A PHE
331A PHE
440A HIS
441A GLY
442A TYR
444A ILE
External LinksHelp

PDB The Protein Data Bank
CSA Catalytic Site Atlas
PDBSum Overview of the macromolecular structure
CATH Protein Structure Classification
Scop Structural Classification of Proteins
Pfam Protein Families and Domains
UniProt Universal Protein Resource

LIGPLOT (only on holo-pages) is hosted at the EBI.

The LigPlot Jmol links point directly to the Jmol visualisation interface provided on the PDBSum page.

Note that due to different software used, the atomic contacts of LigPlot and LigASite do not necessarily correspond.

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Links to external databases:

LigPlot (hosted at the EBI):

Download FilesHelp

Several files are provided for download:

• The XML file defining the residue-ligand contacts; this file contains data on the apo and all holo-structures.
• The XML Schema file defining the semantics of the XML file
• 3D coordinates of the structure used in constructing LigASite (PISA structure file whenever available, PDB file otherwise.
• 3D coordinates of the combined binding residues in the apo structure
• 3D coordinates of the binding residues of the holo structure (only on the holo page)

Coordinate files are in PDB format.

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Hide table of related structures

List of related structure, containing both the apo-structure and other holo-structures.

Column 1 gives the PDB ID and column 2 the unique ID of the ligands (holo-structures only).

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pdb ID
1qif Details
other holo-structures
pdb ID Ligand Unique ID
2c4h ACEM1543 AT3O1540 Details
ACEF1543 AT3H1540
2vt7 PGEN1539 PGEO1540 Details
2wg1 MESA2541 PG4A2547 PG4A2546 Details
FP1A2540 _GBA2539
1qti GNTD_600 Details
1vot HUPB_999 Details
2vjb CCDI1539 Details
2ack EDRD_999 Details
1amn NAFF_594 Details
2wg0 PEGK2549 PG4J2542 _GBI2540 Details
PEGN2549 _GBL2540 PG4M2542
1gpn HUBC1538 Details
2vjc CCDJ1537 Details
1gpk HUPF1540 Details
1oce MF2D_700 Details
2xi4 PGES1004 Details
Ligand ListHelp

Ligands present in this holo structure.

Column 1 shows the ligand HET code
Column 2 shows the name, chemical formula and (non-stereo) SMILES string.

Data in column 2 appears as 'not_found' when it is not present in the file 'pdb2smiles.xml' from

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FORMULA: C10 H16 N1 O1
SMILES: CC[N+](C)(C)c1cccc(O)c1
April 2012
Interdisciplinary Research Institute, Computational Biology, Villeneuve d'Ascq, France
University College London, Biomolecular Structure and Modelling Unit, London, UK
Hospital for Sick Children and University of Toronto, Structural Biology and Biochemistry Program, Toronto, Canada
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