Structure of PDB 1of1 Chain B Binding Site BS01

Receptor Information
>1of1 Chain B (length=313) Species: 10299 (Human alphaherpesvirus 1 strain 17) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MPTLLRVYIDGPHGMGKTTTTQLLVALGSRDDIVYVPEPMTYWRVLGASE
TIANIYTTQHRLDQGEISAGDAAVVMTSAQITMGMPYAVTDAVLAPHIGG
EAPPPALTLIFDRHPIAALLCYPAARYLMGSMTPQAVLAFVALIPPTLPG
TNIVLGALPEDRHIDRLAKRGERLDLAMLAAIRRVYGLLANTVRYLQCGG
SWREDWGQLSGTPQSNAGPRPHIGDTLFTLFRAPELLAPNGDLYNVFAWA
LDVLAKRLRSMHVFILDYDQSPAGCRDALLQLTSGMVQTHVTTPGSIPTI
CDLARTFAREMGE
Ligand information
Ligand IDSCT
InChIInChI=1S/C12H16N2O4/c1-6-4-14(11(18)13-10(6)17)12-2-8(12)7(5-15)9(16)3-12/h4,7-9,15-16H,2-3,5H2,1H3,(H,13,17,18)/t7-,8-,9-,12-/m0/s1
InChIKeyXRMLXZVSFIBRRJ-PEFMBERDSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)[C@]23C[C@H]2[C@@H]([C@H](C3)O)CO
CACTVS 3.341CC1=CN(C(=O)NC1=O)[C@@]23C[C@H](O)[C@@H](CO)[C@@H]2C3
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)C23CC2C(C(C3)O)CO
ACDLabs 10.04O=C1C(=CN(C(=O)N1)C32C(C(CO)C(O)C2)C3)C
CACTVS 3.341CC1=CN(C(=O)NC1=O)[C]23C[CH](O)[CH](CO)[CH]2C3
FormulaC12 H16 N2 O4
Name(SOUTH)-METHANOCARBA-THYMIDINE
ChEMBL
DrugBankDB02921
ZINCZINC000003802232
PDB chain1of1 Chain B Residue 500 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB1of1 Biochemical and Structural Characterization of (South)-Methanocarbathymidine that Specifically Inhibits Growth of Herpes Simplex Virus Type 1 Thymidine Kinase-Transduced Osteosarcoma Cells
Resolution1.95 Å
Binding residue
(original residue number in PDB)		H58 E83 I97 Y101 Q125 M128 R163 A168 Y172 E225
Binding residue
(residue number reindexed from 1)		H13 E38 I52 Y56 Q80 M83 R113 A118 Y122 E172
Annotation score2
Binding affinityMOAD: ic50=15uM
Enzymatic activity
Catalytic site (original residue number in PDB) K62 E83 D162 R163 R220 E225
Catalytic site (residue number reindexed from 1) K17 E38 D112 R113 R170 E172
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:1of1, PDBe:1of1, PDBj:1of1
PDBsum1of1
PubMed15163659
UniProtP0DTH5|KITH_HHV11 Thymidine kinase (Gene Name=TK)

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