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LigASite database of binding sites |
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PDB ID and HEADER , TITLE and
COMPND records of the PDB file. | (click anywhere in this window to remove it) |
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1dcy |
HYDROLASE/HYDROLASE INHIBITOR |
HEADER |
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CRYSTAL STRUCTURE OF HUMAN S-PLA2 IN COMPLEX WITH INDOLE 3 ACTIVE SITE INHIBITOR |
TITLE |
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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. | (click anywhere in this window to remove it) |
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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. | (click anywhere in this window to remove it) |
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I3N H1201 |
2 | E |
LEU |
5 | E |
PHE |
6 | E |
HIS |
9 | E |
ILE |
17 | E |
ALA |
18 | A |
ALA |
19 | A |
LEU |
21 | E |
TYR |
22 | E |
GLY |
23 | A |
PHE |
27 | E |
HIS |
28 | E |
CYS |
29 | E |
GLY |
30 | E |
VAL |
| 44 | E |
CYS |
47 | E |
HIS |
48 | E |
ASP |
51 | E |
TYR |
62 | E |
LYS |
98 | E |
PHE |
111 | A |
TYR |
I3N D1201 |
2 | A |
LEU |
5 | A |
PHE |
6 | A |
HIS |
9 | A |
ILE |
17 | A |
ALA |
18 | E |
ALA |
19 | E |
LEU |
| 21 | A |
TYR |
22 | A |
GLY |
23 | E |
PHE |
27 | A |
HIS |
28 | A |
CYS |
29 | A |
GLY |
30 | A |
VAL |
31 | A |
GLY |
44 | A |
CYS |
47 | A |
HIS |
48 | A |
ASP |
51 | A |
TYR |
62 | A |
LYS |
98 | A |
PHE |
111 | E |
TYR |
| CA C 198 |
27 | A |
HIS |
29 | A |
GLY |
31 | A |
GLY |
48 | A |
ASP |
CA G 198 |
27 | E |
HIS |
29 | E |
GLY |
30 | E |
VAL |
31 | E |
GLY |
48 | E |
ASP |
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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. | (click anywhere in this window to remove it) |
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Links to external databases: LigPlot (hosted at the EBI):
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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. | (click anywhere in this window to remove it) |
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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. | (click anywhere in this window to remove it) |
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pdb ID |
1bbc |
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Details |
pdb ID |
Ligand Unique ID |
1poe |
GELB_935 _CAB_802 |
Details |
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GELA_930 _CAA_801 |
1db5 |
6IND_200 _CAC_198 |
Details |
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6INH_200 _CAG_198 |
1j1a |
_CAG_201 BHPH2301 |
Details |
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BHPD1301 _CAG_201 BHPH2301 _CAC_201 |
1kqu |
BR4D_501 _CAC_301 |
Details |
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BR4H_501 _CAG_301 |
1kvo |
OAPC_190 _CAC_191 |
Details |
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OAPD_190 _CAD_191 |
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OAPB_190 _CAB_191 |
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OAPA_190 _CAA_191 |
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OAPF_190 _CAF_191 |
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OAPE_190 _CAE_191 |
1ayp |
INBB_202 _CAB_303 |
Details |
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INBD_204 _CAD_307 |
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INBC_203 _CAC_305 |
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INBE_205 _CAE_309 |
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INBF_206 _CAF_311 |
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INBA_201 _CAA_301 |
1db4 |
8IND_200 _CAC_198 |
Details |
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8INH_200 _CAG_198 |
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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 . | (click anywhere in this window to remove it) |
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I3N |
NAME: |
1-BENZYL-5-METHOXY-2-METHYL-1H-INDOL-3-YL)-ACETIC ACID |
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FORMULA: |
C19 H19 N1 O3 |
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SMILES: |
COc1ccc2[n](Cc3ccccc3)c(C)c(CC(O)=O)c2c1 |
CA |
NAME: |
CALCIUM ION |
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FORMULA: |
CA1 |
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SMILES: |
[Ca++] |
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v9.3 February 2011 |
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 |
Script execution time: 1.1406 seconds |