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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1rsi
LYASE HEADER
DHNA COMPLEX WITH 2-AMINO-5-BROMO-3-HYDROXY-6- PHENYLPYRIMIDINE 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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977 L1001
5K ILE
18I ALA
19I LEU
22I GLU
48K VAL
51K THR
52K VAL
53K HIS
54K TYR
55K GLY
71I ASN
72I LEU
73I LEU
74I GLU
100I LYS
104I PRO
105I ILE
114I ILE
977 N1001
5M ILE
18O ALA
19O LEU
22O GLU
48M VAL
51M THR
52M VAL
53M HIS
54M TYR
55M GLY
71O ASN
72O LEU
73O LEU
74O GLU
100O LYS
104O PRO
105O ILE
114O ILE
977 B1001
5A ILE
18C ALA
19C LEU
22C GLU
48A VAL
51A THR
52A VAL
53A HIS
54A TYR
55A GLY
71C ASN
72C LEU
73C LEU
74C GLU
100C LYS
104C PRO
105C ILE
114C ILE
977 P1001
5O ILE
18K ALA
19K LEU
22K GLU
48O VAL
51O THR
52O VAL
53O HIS
54O TYR
55O GLY
71K ASN
72K LEU
73K LEU
74K GLU
100K LYS
104K PRO
105K ILE
114K ILE
977 J1001
5I ILE
18M ALA
19M LEU
22M GLU
48I VAL
51I THR
52I VAL
53I HIS
54I TYR
55I GLY
71M ASN
72M LEU
73M LEU
74M GLU
100M LYS
104M PRO
105M ILE
114M ILE
977 H1001
5G ILE
18E ALA
19E LEU
22E GLU
48G VAL
51G THR
52G VAL
53G HIS
54G TYR
55G GLY
71E ASN
72E LEU
73E LEU
74E GLU
100E LYS
104E PRO
105E ILE
114E ILE
977 F1001
5E ILE
18A ALA
19A LEU
22A GLU
48E VAL
51E THR
52E VAL
53E HIS
54E TYR
55E GLY
71A ASN
72A LEU
73A LEU
74A GLU
100A LYS
104A PRO
105A ILE
114A ILE
977 D1001
5C ILE
18G ALA
19G LEU
22G GLU
48C VAL
51C THR
52C VAL
53C HIS
54C TYR
55C GLY
71G ASN
72G LEU
73G LEU
74G GLU
100G LYS
104G PRO
105G ILE
114G 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
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
1rs2 209L1001 Details
209F1001
1rri A45N1001 Details
A45H1001
A45P1001
A45L1001
A45B1001
A45J1001
A45F1001
A45D1001
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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977 NAME: 2-AMINO-5-BROMO-6-PHENYLPYRIMIDIN-4-OL
FORMULA: C10 H8 N3 O1 BR1
SMILES: Nc1nc(O)c(Br)c(n1)c2ccccc2
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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