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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3nxv
OXIDOREDUCTASE HEADER
PREFERENTIAL SELECTION OF ISOMER BINDING FROM CHIRAL MIXTURE ALTERNATE BINDING MODES OBSERVED FOR THE E- AND Z-ISOMERS O OF 5-SUBSTITUTED 2,4-DIAMINOFURO[2,3-D]PYRIMIDINES AS TERNA COMPLEXES WITH NADPH AND HUMAN DIHYDROFOLATE REDUCTASE TITLE
DIHYDROFOLATE REDUCTASE 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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D2F A 187
7A ILE
8A VAL
9A ALA
20A GLY
21A ASP
22A LEU
26A PRO
27A LEU
30A GLU
31A PHE
33A TYR
34A PHE
52A MET
56A THR
59A SER
60A ILE
61A PRO
67A LEU
115A VAL
136A THR
NDP A 188
8A VAL
9A ALA
16A ILE
17A GLY
20A GLY
21A ASP
22A LEU
24A TRP
53A GLY
54A LYS
55A LYS
56A THR
59A SER
75A LEU
76A SER
77A ARG
78A GLU
91A ARG
92A SER
93A LEU
115A VAL
116A GLY
117A GLY
118A SER
119A SER
120A VAL
121A TYR
123A GLU
146A THR
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
1pdb Details
other holo-structures
pdb ID Ligand Unique ID
3nxx D2DA_188 NDPA_187 Details
1pd8 CO4A_301 NDPA_300 Details
2dhf DZFB_187 Details
DZFA_187
1ohk COPA_188 NDPA_187 Details
3ghw GHWA_187 NDPA_188 Details
1ohj COPA_188 NDPA_187 Details
3nu0 3TUA_188 NDPA_187 Details
3ntz 3TZA_187 NDPA_188 Details
1s3v TQDA_187 Details
1dhf FOLB_187 Details
FOLA_187
3nxr D2DA_192 NDPA_187 Details
1s3u TQDA_187 Details
3s7a 684A_192 Details
1pd9 CO4A_187 Details
1kmv LIIA_201 NDPA_202 Details
1s3w NAPA_187 TQTA_188 Details
1kms LIHA_201 NDPA_202 Details
1drf FOLA_187 Details
3nxt SO4A_191 NDPA_187 Details
D2EA_188 SO4A_191 NDPA_187
1u72 MTXA_188 NDPA_187 Details
3nxy D2HA_188 NDPA_187 Details
3nzd D2QA_187 NDPA_188 Details
1hfr MOTA_188 NAPA_187 Details
1yho NDPA_190 TRRA_200 Details
2c2t 39BA1188 NDPA1187 Details
39BB1188 NDPB1187
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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D2F NAME: not_found
FORMULA: not_found
SMILES: not_found
NDP NAME: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
FORMULA: C21 H30 N7 O17 P3
SMILES: NC(=O)C1=CN(C=CC1)C2OC(COP(O)(=O)OP(O)(=O)OCC3OC(C(OP(O)(O)=O)C3O)[n]4cnc5c(N)ncnc45)C(O)C2O
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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