Structure of PDB 4oqm Chain B Binding Site BS01

Receptor Information
>4oqm 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
TNIVLGALPEDRHIDRLAKRPGERLDLAMLAAIRRVYGLLANTVRYLQCG
GSWREDWGQLSGPQSNAGPRPHIGDTLFTLFRAPELLAPNGDLYNVFAWA
LDVLAKRLRSMHVFILDYDQSPAGCRDALLQLTSGMVQTHVTTPGSIPTI
CDLARTFAREMGE
Ligand information
Ligand IDFDU
InChIInChI=1S/C11H11FN2O5/c1-2-5-3-14(11(18)13-9(5)17)10-7(12)8(16)6(4-15)19-10/h1,3,6-8,10,15-16H,4H2,(H,13,17,18)/t6-,7+,8-,10-/m1/s1
InChIKeyYEEGMPUOCRQFRV-IBCQBUCCSA-N
SMILES
SoftwareSMILES
CACTVS 3.370OC[CH]1O[CH]([CH](F)[CH]1O)N2C=C(C#C)C(=O)NC2=O
ACDLabs 12.01O=C1NC(=O)N(C=C1C#C)C2OC(C(O)C2F)CO
CACTVS 3.370OC[C@H]1O[C@H]([C@@H](F)[C@@H]1O)N2C=C(C#C)C(=O)NC2=O
OpenEye OEToolkits 1.7.6C#CC1=CN(C(=O)NC1=O)[C@H]2[C@H]([C@@H]([C@H](O2)CO)O)F
OpenEye OEToolkits 1.7.6C#CC1=CN(C(=O)NC1=O)C2C(C(C(O2)CO)O)F
FormulaC11 H11 F N2 O5
Name1-(2-deoxy-2-fluoro-beta-D-arabinofuranosyl)-5-ethynylpyrimidine-2,4(1H,3H)-dione;
(2'S)-2'-DEOXY-2'-FLUORO-5-ETHYNYLURIDINE
ChEMBLCHEMBL2368299
DrugBank
ZINCZINC000026721200
PDB chain4oqm Chain B Residue 501 [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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PDB4oqm Dynamic metabolic labeling of DNA in vivo with arabinosyl nucleosides.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		H58 E83 Y101 Q125 M128 R163 A168 Y172 E225
Binding residue
(residue number reindexed from 1)		H13 E38 Y56 Q80 M83 R113 A118 Y122 E173
Annotation score2
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 E173
Enzyme Commision number 2.7.1.21: thymidine kinase.
Gene Ontology
Molecular Function
GO:0004797 thymidine kinase activity
GO:0005524 ATP binding
Biological Process
GO:0006230 TMP biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4oqm, PDBe:4oqm, PDBj:4oqm
PDBsum4oqm
PubMed
UniProtP0DTH5|KITH_HHV11 Thymidine kinase (Gene Name=TK)

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