university lille north of france LigASite database of binding sites
apo-structureHelp

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

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1hcl
PROTEIN KINASE HEADER
HUMAN CYCLIN-DEPENDENT KINASE 2 TITLE
HUMAN CYCLIN-DEPENDENT KINASE 2 COMPND
Illustration of Binding SiteHelp

Figure highlighting the binding site residues. Figures were drawn with Molscript (7) and rendered with Raster3D (8). PISA coordinates (3) are used when available (all entries except NMR).

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Contacting ResiduesHelp

List of binding site residues detected in this protein.

Column 1 gives the position, coloured on a yellow-to-red scale depending on the fraction of corresponding holo-structures where the residue is in contact with a ligand.
Column 2 gives the 3-letter amino acid code, coloured according to physico-chemical type.

Chain ID's of residues are not mentioned in this page because all chains in the apo-structure refer to the same protein.

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8 GLU
9 LYS
10 ILE
11 GLY
12 GLU
13 GLY
14 THR
15 TYR
16 GLY
18 VAL
20 LYS
31 ALA
33 LYS
35 ILE
47 THR
51 GLU
55 LEU
64 VAL
80 PHE
81 GLU
82 PHE
83 LEU
84 HIS
85 GLN
86 ASP
88 LYS
89 LYS
127 ASP
129 LYS
131 GLN
132 ASN
134 LEU
144 ALA
145 ASP
146 PHE
147 GLY
148 LEU
158 THR
162 GLU
164 VAL
290 THR
298 LEU
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:

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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holo-structuresHelp

Table describing the holo-structures and ligands used to define the binding sites.

Column 1 gives the PDB ID of the holo-structure.
Column 2 gives the unique ID of the ligand; a space-separated list of HET-groups that constitute the ligand (see Methods). Each HET-group in the ligand is uniquely identified by a string in which the first four characters are the three-letter HET ID from the PDB file followed by the chain ID from the PISA file, and the last four characters are the residue sequence number from the PDB file.
Column 3 gives the number of atoms in each ligand.
Column 4 gives the number of protein-ligand inter-atomic contacts.

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pdb ID Ligand Unique ID #atoms #contacts
3lfs A07A_299 22 100 Details
2xmy CDKA_500 29 129 Details
2vto LZ8A1299 24 117 Details
2a4l RRCA_300 26 122 Details
1ke7 LS3A_299 28 125 Details
2vu3 LZEA1299 25 99 Details
2vtq LZAA1299 25 112 Details
3lfq A28A_299 23 108 Details
3fz1 B98A_299 19 98 Details
1pf8 SU9A_500 18 91 Details
1fin ATPB_299 31 92 Details
1pye PM1A_700 28 109 Details
1h0v UN4A1299 18 90 Details
1pxo CK7A_500 14 81 Details
2v22 C35C1433 55 137 Details
2vtn LZ7A1299 19 98 Details
2c6l DT4A1299 28 120 Details
1pxl CK4A_500 24 121 Details
3le6 2BZA_299 25 115 Details
1dm2 HMDA_400 19 91 Details
1ke6 LS2A_299 27 124 Details
2c6t DT5B1297 27 116 Details
2bhh RYUA1299 31 124 Details
2b54 D05A_300 30 121 Details
2vth LZ2A1300 15 77 Details
2r64 740A_500 32 146 Details
2c6k DT2A1299 27 115 Details
1p2a 5BNA_301 23 117 Details
2c5n CK8E1298 23 112 Details
CK8B1297 23 119
1gih 1PUA_501 23 109 Details
2c68 CT6A1297 24 128 Details
1y8y CT7A_401 21 88 Details
2c6m DT5A1297 27 117 Details
2btr U73A_300 18 87 Details
1fvt 106A_299 23 105 Details
1fq1 ATPC_381 _MGD_383 32 141 Details
2exm ZIPA_400 15 79 Details
1jsv U55A_400 18 81 Details
2uzb C75B1297 24 116 Details
2c69 CT8A1299 24 116 Details
2bhe BRYA1299 21 99 Details
3unk 0BYA_299 24 113 Details
3unj 0BXA_299 23 125 Details
2c5v CK4B1297 24 127 Details
2vtj LZ4A1300 18 81 Details
2b55 D31A_299 31 124 Details
1jst ATPB_300 _MNC_299 32 127 Details
1pxm CK5A_500 21 107 Details
1ykr 628A_299 30 127 Details
1h01 FALA_301 GOLA_300 36 152 Details
1pxk CK3A_500 17 96 Details
2vtp LZ9A1299 26 113 Details
3lfn A27A_299 28 135 Details
2a0c CK9X_500 27 120 Details
2uzo C62A1297 23 104 Details
2fvd LIAA_299 30 112 Details
3s2p PMUA_500 24 104 Details
2vts LZCA1299 23 115 Details
1pxi CK1A_500 14 70 Details
2vtr LZBA1299 16 74 Details
1pxp CK8A_500 23 117 Details
2uze C95B1297 22 112 Details
1di8 DTQA_500 22 118 Details
2vtl LZ5A1299 14 72 Details
2xnb Y8LA1299 27 126 Details
2uzd C85B1297 23 120 Details
2vtt LZDA1299 25 113 Details
2c6o 4SPA1297 28 134 Details
1ol1 CIRE_500 CIRF_501 22 79 Details
3ns9 NS9A___0 28 120 Details
2c5y MTWA1298 28 124 Details
2uzl C94B1297 27 116 Details
3eid PO5A_299 36 166 Details
1vyz N5BA_300 17 89 Details
2w05 FRTA1299 30 126 Details
2bts U32A1299 19 89 Details
1ke9 LS5A_299 25 112 Details
1pxn CK6A_500 22 106 Details
2b53 D23A_299 26 125 Details
3ej1 5BPA_299 19 97 Details
2i40 BLZB_301 31 123 Details
2clx F18A1299 16 89 Details
2x1n X1NA1297 24 127 Details
1r78 FMDA_299 28 119 Details
2b52 D42A_299 31 145 Details
1ke8 LS4A_299 27 116 Details
2w1h L0HA1299 23 118 Details
2duv 371A_501 28 134 Details
1hck ATPA_400 _MGA_401 32 125 Details
2vti LZ3A1299 22 107 Details
1h0w 207A1299 18 82 Details
1ckp EDOA_300 PVBA_299 22 109 Details
1y91 CT9A_401 33 142 Details
1ke5 LS1A_299 23 110 Details
3f5x EZVK_300 32 145 Details
EZVH_300 32 142
EZVD_300 32 137
EZVA_300 32 145
2wev CK7B1297 23 113 Details
1w0x OLOC1299 22 108 Details
2j9m PY8A_299 22 100 Details
3eoc T2AA_501 29 129 Details
2v0d C53A1299 14 72 Details
2uzn C96A1299 24 114 Details
1aq1 STUA_299 35 126 Details
2cjm ATPB1298 31 131 Details
2c6i DT1A1299 28 123 Details
1fvv 107B_601 31 130 Details
1g5s I17A_400 30 138 Details
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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