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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1rri
LYASE HEADER
DHNA COMPLEX WITH 3-(5-AMINO-7-HYDROXY-[1,2,3] TRIAZOLO [4, 5-D]PYRIMIDIN-2-YL)-BENZOIC ACID 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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A45 N1001
13M TYR
14M GLY
15M TYR
16M HIS
58C PHE
62C LYS
65M MET
66M GLU
67M GLY
68M LYS
69M ALA
106G PRO
107G GLY
108G HIS
A45 H1001
13G TYR
14G GLY
15G TYR
16G HIS
58I PHE
62I LYS
65G MET
66G GLU
67G GLY
68G LYS
69G ALA
106M PRO
107M GLY
108E HIS
A45 P1001
13O TYR
14O GLY
15O TYR
16O HIS
58A PHE
62A LYS
65O MET
66O GLU
67O GLY
68O LYS
69O ALA
106C PRO
107C GLY
108K HIS
A45 L1001
13K TYR
14K GLY
15K TYR
16K HIS
58E PHE
62E LYS
65K MET
66K GLU
67K GLY
68K LYS
69K ALA
106A PRO
107A GLY
108A HIS
A45 B1001
13A TYR
14A GLY
15A TYR
16A HIS
58O PHE
62O LYS
65A MET
66A GLU
67A GLY
68A LYS
69A ALA
106K PRO
107K GLY
108C HIS
A45 J1001
13I TYR
14I GLY
15I TYR
16I HIS
58G PHE
62G LYS
65I MET
66I GLU
67I GLY
68I LYS
69I ALA
106E PRO
107E GLY
108M HIS
A45 F1001
13E TYR
14E GLY
15E TYR
16E HIS
58K PHE
62K LYS
65E MET
66E GLU
67E GLY
68E LYS
69E ALA
106I PRO
107I GLY
108I HIS
A45 D1001
13C TYR
14C GLY
15C TYR
16C HIS
58M PHE
62M LYS
65C MET
66C GLU
67C GLY
68C LYS
69C ALA
106O PRO
107O GLY
108O HIS
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).

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apo-structure
pdb ID
1dhn Details
other holo-structures
pdb ID Ligand Unique ID
1rsd PSBJ1001 Details
PSBL1001
PSBN1001
PSBH1001
PSBB1001
PSBD1001
PSBF1001
PSBP1001
1rs4 45PJ1001 Details
45PL1001
45PF1001
45PN1001
45PH1001
45PB1001
45PD1001
45PP1001
2dhn PH2N_122 Details
PH2P_122
PH2J_122
PH2D_122
PH2B_122
PH2H_122
1u68 NPRL1001 Details
NPRJ1001
NPRP1001
NPRH1001
NPRD1001
NPRF1001
NPRB1001
NPRN1001
2nm3 MPUK_131 Details
MPUE_131
MPUN_131
MPUB_131
MPUT_131
MPUW_131
MPUH_131
MPUQ_131
2nm2 NEUF_122 Details
NEUN_322
NEUP_422
NEUB_122
NEUD_222
NEUH_222
NEUL_422
NEUJ_322
1rsi 977L1001 Details
977N1001
977B1001
977P1001
977J1001
977H1001
977F1001
977D1001
1rs2 209L1001 Details
209F1001
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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A45 NAME: 3-(5-AMINO-7-HYDROXY-[1,2,3]TRIAZOLO[4,5-D]PYRIMIDIN-2-YL)-BENZOIC ACID
FORMULA: C11 H8 N6 O3
SMILES: Nc1nc(O)c2n[n](nc2n1)c3cccc(c3)C(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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