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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3f5x
TRANSFERASE/CELL CYCLE HEADER
CDK-2-CYCLIN COMPLEX WITH INDAZOLE INHIBITOR 9 BOUND AT ITS ACTIVE SITE TITLE
CELL DIVISION PROTEIN KINASE 2 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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EZV K 300
8K GLU
10K ILE
11K GLY
18K VAL
31K ALA
33K LYS
51K GLU
55K LEU
64K VAL
80K PHE
81K GLU
82K PHE
83K LEU
84K HIS
85K GLN
86K ASP
89K LYS
131K GLN
134K LEU
144K ALA
145K ASP
146K PHE
EZV D 300
8D GLU
10D ILE
11D GLY
18D VAL
31D ALA
33D LYS
51D GLU
55D LEU
64D VAL
80D PHE
81D GLU
82D PHE
83D LEU
84D HIS
85D GLN
86D ASP
89D LYS
131D GLN
134D LEU
144D ALA
145D ASP
146D PHE
EZV H 300
10H ILE
11H GLY
18H VAL
31H ALA
33H LYS
51H GLU
55H LEU
64H VAL
80H PHE
81H GLU
82H PHE
83H LEU
84H HIS
85H GLN
86H ASP
89H LYS
131H GLN
134H LEU
144H ALA
145H ASP
146H PHE
EZV A 300
10A ILE
11A GLY
18A VAL
31A ALA
33A LYS
51A GLU
55A LEU
64A VAL
80A PHE
81A GLU
82A PHE
83A LEU
84A HIS
85A GLN
86A ASP
89A LYS
131A GLN
134A LEU
144A ALA
145A ASP
146A PHE
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
1pw2 Details
other holo-structures
pdb ID Ligand Unique ID
3lfs A07A_299 Details
2xmy CDKA_500 Details
2vto LZ8A1299 Details
2a4l RRCA_300 Details
1ke7 LS3A_299 Details
2vu3 LZEA1299 Details
2vtq LZAA1299 Details
3lfq A28A_299 Details
3fz1 B98A_299 Details
1pf8 SU9A_500 Details
1fin ATPB_299 Details
1pye PM1A_700 Details
1h0v UN4A1299 Details
1pxo CK7A_500 Details
2v22 C35C1433 Details
2vtn LZ7A1299 Details
2c6l DT4A1299 Details
1pxl CK4A_500 Details
3le6 2BZA_299 Details
1dm2 HMDA_400 Details
1ke6 LS2A_299 Details
2c6t DT5B1297 Details
2bhh RYUA1299 Details
2b54 D05A_300 Details
2vth LZ2A1300 Details
2r64 740A_500 Details
2c6k DT2A1299 Details
1p2a 5BNA_301 Details
2c5n CK8E1298 Details
CK8B1297
1gih 1PUA_501 Details
2c68 CT6A1297 Details
1y8y CT7A_401 Details
2c6m DT5A1297 Details
2btr U73A_300 Details
1fvt 106A_299 Details
1fq1 ATPC_381 _MGD_383 Details
2exm ZIPA_400 Details
1jsv U55A_400 Details
2uzb C75B1297 Details
2c69 CT8A1299 Details
2bhe BRYA1299 Details
3unk 0BYA_299 Details
3unj 0BXA_299 Details
2c5v CK4B1297 Details
2vtj LZ4A1300 Details
2b55 D31A_299 Details
1jst ATPB_300 _MNC_299 Details
1pxm CK5A_500 Details
1ykr 628A_299 Details
1h01 FALA_301 GOLA_300 Details
1pxk CK3A_500 Details
2vtp LZ9A1299 Details
3lfn A27A_299 Details
2a0c CK9X_500 Details
2uzo C62A1297 Details
2fvd LIAA_299 Details
3s2p PMUA_500 Details
2vts LZCA1299 Details
1pxi CK1A_500 Details
2vtr LZBA1299 Details
1pxp CK8A_500 Details
2uze C95B1297 Details
1di8 DTQA_500 Details
2vtl LZ5A1299 Details
2xnb Y8LA1299 Details
2uzd C85B1297 Details
2vtt LZDA1299 Details
2c6o 4SPA1297 Details
1ol1 CIRE_500 CIRF_501 Details
3ns9 NS9A___0 Details
2c5y MTWA1298 Details
2uzl C94B1297 Details
3eid PO5A_299 Details
1vyz N5BA_300 Details
2w05 FRTA1299 Details
2bts U32A1299 Details
1ke9 LS5A_299 Details
1pxn CK6A_500 Details
2b53 D23A_299 Details
3ej1 5BPA_299 Details
2i40 BLZB_301 Details
2clx F18A1299 Details
2x1n X1NA1297 Details
1r78 FMDA_299 Details
2b52 D42A_299 Details
1ke8 LS4A_299 Details
2w1h L0HA1299 Details
2duv 371A_501 Details
1hck ATPA_400 _MGA_401 Details
2vti LZ3A1299 Details
1h0w 207A1299 Details
1ckp EDOA_300 PVBA_299 Details
1y91 CT9A_401 Details
1ke5 LS1A_299 Details
2wev CK7B1297 Details
1w0x OLOC1299 Details
2j9m PY8A_299 Details
3eoc T2AA_501 Details
2v0d C53A1299 Details
2uzn C96A1299 Details
1aq1 STUA_299 Details
2cjm ATPB1298 Details
2c6i DT1A1299 Details
1fvv 107B_601 Details
1g5s I17A_400 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 www.rcsb.org.

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EZV NAME: not_found
FORMULA: not_found
SMILES: not_found
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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