Structure of PDB 3vtk Chain A Binding Site BS02

Receptor Information
>3vtk Chain A (length=313) Species: 10304 (Human alphaherpesvirus 1 strain F) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MPTLLRVYIDGPHGMGKTTTTQLLVALGSRDDIVYVPEPMTYWRVLGASE
TIANIYTTQHRLDQGEISAGDAAVVMTSAQITMGMPYAVTDAVLAPHIGG
EAGSPPPALTLIFDRHPIAALLCYPAARYLMGSMTPQAVLAFVALIPPTL
PGTNIVLGALPEDRHIDRLAKRQRPGERLDLAMLAAIRRVYGLLANTVRY
LQCGGSWREDWGQLSGPRPHIGDTLFTLFRAPELLAPNGDLYNVFAWALD
VLAKRLRSMHVFILDYDQSPAGCRDALLQLTSGMVQTHVTTPGSIPTICD
LARTFAREMGEAN
Ligand information
Ligand ID5IU
InChIInChI=1S/C9H12IN2O8P/c10-4-2-12(9(15)11-8(4)14)7-1-5(13)6(20-7)3-19-21(16,17)18/h2,5-7,13H,1,3H2,(H,11,14,15)(H2,16,17,18)/t5-,6+,7+/m0/s1
InChIKeyWXFYBFRZROJDLL-RRKCRQDMSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C1C(C(OC1N2C=C(C(=O)NC2=O)I)COP(=O)(O)O)O
CACTVS 3.341O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=C(I)C(=O)NC2=O
OpenEye OEToolkits 1.5.0C1[C@@H]([C@H](O[C@H]1N2C=C(C(=O)NC2=O)I)COP(=O)(O)O)O
ACDLabs 10.04IC=1C(=O)NC(=O)N(C=1)C2OC(C(O)C2)COP(=O)(O)O
CACTVS 3.341O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)N2C=C(I)C(=O)NC2=O
FormulaC9 H12 I N2 O8 P
Name5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
ChEMBLCHEMBL1160594
DrugBankDB02324
ZINC
PDB chain3vtk Chain A Residue 500 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3vtk The structures of thymidine kinase from herpes simplex virus type 1 in complex with substrates and a substrate analogue.
Resolution3.0 Å
Binding residue
(original residue number in PDB)		H58 K62 E83 W88 I97 Y101 Q125 M128 R163 A168 Y172 E225
Binding residue
(residue number reindexed from 1)		H13 K17 E38 W43 I52 Y56 Q80 M83 R115 A120 Y124 E177
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) K62 E83 D162 R163 R220 R222 E225
Catalytic site (residue number reindexed from 1) K17 E38 D114 R115 R172 R174 E177
Enzyme Commision number 2.7.1.21: thymidine kinase.
Gene Ontology
Molecular Function
GO:0004797 thymidine kinase activity
GO:0005524 ATP binding
GO:0016301 kinase activity
Biological Process
GO:0006230 TMP biosynthetic process
GO:0009157 deoxyribonucleoside monophosphate biosynthetic process
GO:0016310 phosphorylation
GO:0071897 DNA biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3vtk, PDBe:3vtk, PDBj:3vtk
PDBsum3vtk
PubMed9336833
UniProtP0DTH5|KITH_HHV11 Thymidine kinase (Gene Name=TK)

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