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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1rsd
LYASE HEADER
DHNA COMPLEX WITH 3-(5-AMINO-7-HYDROXY-[1,2,3]TRIAZOLO[4,5- D]PYRIMIDIN-2-YL)-N-[2-(2-HYDROXYMETHYL-PHENYLSULFANYL)- BENZYL]-BENZAMIDE TITLE
DIHYDRONEOPTERIN ALDOLASE 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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PSB P1001
5G ILE
15E TYR
18H ALA
19H LEU
22H GLU
24E GLU
25E ILE
48G VAL
51G THR
52G VAL
53G HIS
54G TYR
55G GLY
56G GLU
59G GLU
62G LYS
71H ASN
72H LEU
73H LEU
74H GLU
100H LYS
104H PRO
105H ILE
106H PRO
114H ILE
PSB J1001
5E ILE
15G TYR
18B ALA
19B LEU
22B GLU
24G GLU
25G ILE
48E VAL
51E THR
52E VAL
53E HIS
54E TYR
55E GLY
56E GLU
59E GLU
62E LYS
71B ASN
72B LEU
73B LEU
74B GLU
100B LYS
104B PRO
105B ILE
106B PRO
114B ILE
PSB I1001
5B ILE
15D TYR
18A ALA
19A LEU
22A GLU
24D GLU
25D ILE
48B VAL
51B THR
52B VAL
53B HIS
54B TYR
55B GLY
56B GLU
59B GLU
62B LYS
71A ASN
72A LEU
73A LEU
74A GLU
100A LYS
104A PRO
105A ILE
106A PRO
114A ILE
PSB M1001
5C ILE
15H TYR
18E ALA
19E LEU
22E GLU
24H GLU
25H ILE
48C VAL
51C THR
52C VAL
53C HIS
54C TYR
55C GLY
56C GLU
59C GLU
62C LYS
71E ASN
72E LEU
73E LEU
74E GLU
100E LYS
104E PRO
105E ILE
106E PRO
114E ILE
PSB O1001
5D ILE
15B TYR
18G ALA
19G LEU
22G GLU
24B GLU
25B ILE
48D VAL
51D THR
52D VAL
53D HIS
54D TYR
55D GLY
56D GLU
59D GLU
62D LYS
71G ASN
72G LEU
73G LEU
74G GLU
100G LYS
104G PRO
105G ILE
106G PRO
114G ILE
PSB K1001
5A ILE
15F TYR
18C ALA
19C LEU
22C GLU
24F GLU
25F ILE
48A VAL
51A THR
52A VAL
53A HIS
54A TYR
55A GLY
56A GLU
59A GLU
62A LYS
71C ASN
72C LEU
73C LEU
74C GLU
100C LYS
104C PRO
105C ILE
106C PRO
114C ILE
PSB N1001
5H ILE
15C TYR
18F ALA
19F LEU
22F GLU
24C GLU
25C ILE
48H VAL
51H THR
52H VAL
53H HIS
54H TYR
55H GLY
56H GLU
59H GLU
62H LYS
71F ASN
72F LEU
73F LEU
74F GLU
100F LYS
104F PRO
105F ILE
106F PRO
114F ILE
PSB L1001
5F ILE
15A TYR
18D ALA
19D LEU
22D GLU
24A GLU
25A ILE
48F VAL
51F THR
52F VAL
53F HIS
54F TYR
55F GLY
56F GLU
59F GLU
62F LYS
71D ASN
72D LEU
73D LEU
74D GLU
100D LYS
104D PRO
105D ILE
106D PRO
114D 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):

» Jmol
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
1dhn Details
other holo-structures
pdb ID Ligand Unique ID
2nm2 NEUF_122 Details
NEUA_122
NEUD_422
NEUB_222
NEUE_222
NEUC_322
NEUH_322
NEUG_422
1rsi 977O1001 Details
977L1001
977I1001
977J1001
977N1001
977P1001
977K1001
977M1001
2nm3 MPUF_131 Details
MPUB_131
MPUE_131
MPUC_131
MPUA_131
MPUG_131
MPUH_131
MPUD_131
1rs2 209O1001 Details
209I1001
1u68 NPRL1001 Details
NPRP1001
NPRO1001
NPRJ1001
NPRI1001
NPRK1001
NPRN1001
NPRM1001
1rs4 45PK1001 Details
45PL1001
45PJ1001
45PP1001
45PI1001
45PO1001
45PN1001
45PM1001
1rri A45N1001 Details
A45K1001
A45P1001
A45O1001
A45L1001
A45J1001
A45M1001
A45I1001
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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PSB NAME: 3-(5-AMINO-7-HYDROXY-[1,2,3]TRIAZOLO[4,5-D]PYRIMIDIN-2-YL)-N-[2-(2-(HYDROXYMETHYL-PHENYLSULFANYL)-BENZYL]-BENZAMIDE
FORMULA: C25 H21 N7 O3 S1
SMILES: Nc1nc(O)c2n[n](nc2n1)c3cccc(c3)C(=O)NCc4ccccc4Sc5ccccc5CO
v3.0
January 2008
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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