Structure of PDB 2orv Chain A Binding Site BS02

Receptor Information
>2orv Chain A (length=163) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RGQIQVILGPMFSGKSTELMRRVRRFQIAQYKCLVIKYAKDTRYMEALPA
CLLRDVAQEALGVAVIGIDEGQFFPDIVEFCEAMANAGKTVIVAALDGTF
QRKPFGAILNLVPLAESVVKLTAVCMECFREAAYTKRLGTEKEVEVIGGA
DKYHSVCRLCYFK
Ligand information
Ligand ID4TA
InChIInChI=1S/C20H29N7O20P4/c1-8-3-26(20(32)25-18(8)31)12-2-9(28)10(43-12)4-41-48(33,34)45-50(37,38)47-51(39,40)46-49(35,36)42-5-11-14(29)15(30)19(44-11)27-7-24-13-16(21)22-6-23-17(13)27/h3,6-7,9-12,14-15,19,28-30H,2,4-5H2,1H3,(H,33,34)(H,35,36)(H,37,38)(H,39,40)(H2,21,22,23)(H,25,31,32)/p-4/t9-,10+,11+,12+,14+,15+,19+/m0/s1
InChIKeyWLGHSSFVEUABFP-SLFMBYJQSA-J
SMILES
SoftwareSMILES
CACTVS 3.385CC1=CN([CH]2C[CH](O)[CH](CO[P]([O-])(=O)O[P]([O-])(=O)O[P]([O-])(=O)O[P]([O-])(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)O2)C(=O)NC1=O
OpenEye OEToolkits 1.7.5CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)([O-])OP(=O)([O-])OP(=O)([O-])OP(=O)([O-])OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)O
OpenEye OEToolkits 1.7.5CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)([O-])OP(=O)([O-])OP(=O)([O-])OP(=O)([O-])OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)O
CACTVS 3.385CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P]([O-])(=O)O[P]([O-])(=O)O[P]([O-])(=O)O[P]([O-])(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)O2)C(=O)NC1=O
FormulaC20 H25 N7 O20 P4
NameP1-(5'-ADENOSYL)P4-(5'-(2'-DEOXY-THYMIDYL))TETRAPHOSPHATE
ChEMBL
DrugBank
ZINC
PDB chain2orv Chain A Residue 801 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2orv Binding of ATP to TK1-like Enzymes Is Associated with a Conformational Change in the Quaternary Structure.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		M28 F29 S30 G31 K32 S33 D58 R60 D97 E98 Q100 F101 L124 T127 F128 F133 V172 E173 V174 I175 G176 Y181
Binding residue
(residue number reindexed from 1)		M11 F12 S13 G14 K15 S16 D41 R43 D69 E70 Q72 F73 L96 T99 F100 F105 V144 E145 V146 I147 G148 Y153
Annotation score3
Binding affinityMOAD: Kd=29nM
Enzymatic activity
Enzyme Commision number 2.7.1.21: thymidine kinase.
Gene Ontology
Molecular Function
GO:0004797 thymidine kinase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0008270 zinc ion binding
GO:0016301 kinase activity
GO:0042802 identical protein binding
GO:0046872 metal ion binding
Biological Process
GO:0006139 nucleobase-containing compound metabolic process
GO:0009157 deoxyribonucleoside monophosphate biosynthetic process
GO:0016310 phosphorylation
GO:0046104 thymidine metabolic process
GO:0046105 thymidine biosynthetic process
GO:0051289 protein homotetramerization
GO:0071897 DNA biosynthetic process
GO:1904860 DNA synthesis involved in mitotic DNA replication
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:2orv, PDBe:2orv, PDBj:2orv
PDBsum2orv
PubMed17407781
UniProtP04183|KITH_HUMAN Thymidine kinase, cytosolic (Gene Name=TK1)

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