university lille north of france LigASite database of binding sites

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

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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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NAI N1374
118M GLU
127M LEU
130M LEU
131M ALA
133M MET
134M SER
137M ALA
174M ILE
175M GLY
177M GLY
178M THR
179M ALA
197M LEU
198M ASP
199M ILE
200M ASN
203M LYS
220M SER
225M LEU
238M ALA
239M VAL
240M LEU
241M VAL
242M PRO
247M PRO
249M LEU
267M ILE
268M ALA
269M ILE
270M ASP
271M GLN
298M VAL
299M ALA
301M MET
302M PRO
NAI L1374
118K GLU
127K LEU
130K LEU
131K ALA
133K MET
134K SER
137K ALA
174K ILE
175K GLY
177K GLY
178K THR
179K ALA
180K GLY
197K LEU
198K ASP
199K ILE
200K ASN
203K LYS
220K SER
225K LEU
238K ALA
239K VAL
240K LEU
241K VAL
242K PRO
247K PRO
249K LEU
267K ILE
268K ALA
269K ILE
270K ASP
271K GLN
298K VAL
299K ALA
301K MET
302K PRO
NAI J1371
130I LEU
131I ALA
133I MET
134I SER
137I ALA
174I ILE
175I GLY
177I GLY
178I THR
179I ALA
180I GLY
197I LEU
198I ASP
199I ILE
200I ASN
203I LYS
220I SER
225I LEU
238I ALA
239I VAL
240I LEU
241I VAL
247I PRO
249I LEU
267I ILE
268I ALA
269I ILE
270I ASP
271I GLN
298I VAL
299I ALA
301I MET
302I PRO
NAI E1372
130D LEU
131D ALA
133D MET
134D SER
137D ALA
174D ILE
175D GLY
177D GLY
178D THR
179D ALA
180D GLY
197D LEU
198D ASP
199D ILE
200D ASN
203D LYS
220D SER
225D LEU
238D ALA
239D VAL
240D LEU
241D VAL
242D PRO
247D PRO
249D LEU
267D ILE
268D ALA
269D ILE
270D ASP
271D GLN
298D VAL
299D ALA
301D MET
302D PRO
NAI G1372
130F LEU
131F ALA
133F MET
134F SER
137F ALA
174F ILE
175F GLY
177F GLY
178F THR
179F ALA
197F LEU
198F ASP
199F ILE
200F ASN
203F LYS
220F SER
238F ALA
239F VAL
240F LEU
241F VAL
242F PRO
247F PRO
249F LEU
267F ILE
268F ALA
269F ILE
270F ASP
271F GLN
298F VAL
299F ALA
300F ASN
301F MET
302F PRO
NAI B1373
130A LEU
131A ALA
133A MET
134A SER
137A ALA
174A ILE
175A GLY
177A GLY
178A THR
179A ALA
180A GLY
197A LEU
198A ASP
199A ILE
200A ASN
203A LYS
220A SER
225A LEU
238A ALA
239A VAL
240A LEU
241A VAL
242A PRO
246A ALA
247A PRO
249A LEU
267A ILE
268A ALA
269A ILE
270A ASP
271A GLN
298A VAL
299A ALA
301A MET
302A PRO
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

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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pdb ID
2vhy Details
other holo-structures
pdb ID Ligand Unique ID
2vhx NADO1376 PYRQ1375 Details
NADL1375 PYRM1374
2vhz NAID1372 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

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FORMULA: C21 H29 N7 O14 P2
SMILES: NC(=O)C1=CN(C=CC1)C2OC(COP(O)(=O)OP(O)(=O)OCC3OC(C(O)C3O)[n]4cnc5c(N)ncnc45)C(O)C2O
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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