university lille north of france LigASite database of binding sites
holo-structureHelp

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

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1eed
ASPARTIC PROTEINASE HEADER
X-RAY CRYSTALLOGRAPHIC ANALYSIS OF INHIBITION OF ENDOTHIAPEPSIN BY CYCLOHEXYL RENIN INHIBITORS TITLE
ENDOTHIAPEPSIN COMPND
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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FOG C 3
7A ILE
8A ASP
12A ASP
13A ALA
76A GLY
77A ASP
114A ASP
117A ILE
217A GLY
218A THR
219A THR
220A LEU
222A TYR
BOC D 4
12A ASP
77A ASP
219A THR
220A LEU
222A TYR
275A PHE
284A PHE
CHS B 1
30A ASP
32A ASP
34A GLY
75A TYR
76A GLY
77A ASP
79A SER
111A PHE
117A ILE
120A LEU
189A PHE
213A ILE
215A ASP
217A GLY
218A THR
301A 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
Help

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).

Clicking the blue 'Hide table of related structures' button removes the entire table.

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apo-structure
pdb ID
4ape Details
other holo-structures
pdb ID Ligand Unique ID
1epp DCIE_333 STAE_332 MTFE_334 LYSE_331 PHEE_330 MASE_329 Details
2v00 ACTA1335 V15A1336 GOLA1332 Details
ACTA1334 V15A1336 GOLA1332
3q6y DMSA4001 S47A5001 Details
3prs 1PEA2001 RITA1001 DMSA5001 Details
3pww ROCA1001 Details
3pb5 F63A1001 Details
4er1 BNAB___1 Details
1e82 HFAB___2 SMCB___3 PCHC___4 MRMB___1 Details
3psy PG4A4001 RB9A1001 Details
DMSA2001 PG4A4001 RB9A1001
3pgi F41A2001 Details
3pm4 F5NA2001 Details
3pi0 DMSA4001 F91A2001 Details
3pmu F7LA2001 Details
3pmy 41LA2001 Details
1od1 DPHB_401 TSMB_400 Details
3pbz DMSA4001 F02A1001 Details
1e81 CPYC___4 SMCB___3 HFAB___2 MRMB___1 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 www.rcsb.org.

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BOC NAME: TERT-BUTYLOXYCARBONYL GROUP
FORMULA: C5 H9 O2
SMILES: CC(C)(C)OC=O
FOG NAME: PHENYLALANINOYL-[1-HYDROXY]-2-PROPYLENE
FORMULA: C12 H15 N1 O2
SMILES: NC(Cc1ccccc1)C(=O)C=CCO
CHS NAME: 4-AMINO-5-CYCLOHEXYL-3-HYDROXY-PENTANOIC ACID
FORMULA: C11 H21 N1 O3
SMILES: NC(CC1CCCCC1)C(O)CC(O)=O
v9.7
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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