Structure of PDB 4jby Chain B Binding Site BS01

Receptor Information
>4jby Chain B (length=315) 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
TNIVLGALPEDRHIDRLAKRQRPGERLDLAMLAAIRRVYGLLANTVRYLQ
CGGSWREDWGQLSGPQSNAGPRPHIGDTLFTLFRAPELLAPNGDLYNVFA
WALDVLAKRLRSMHVFILDYDQSPAGCRDALLQLTSGMVQTHVTTPGSIP
TICDLARTFAREMGE
Ligand information
Ligand IDFSK
InChIInChI=1S/C10H13FN2O3/c1-6-8(3-7(4-11)5-14)13(2)10(16)12-9(6)15/h3,14H,4-5H2,1-2H3,(H,12,15,16)/b7-3+
InChIKeyNEZZLCCSEJKABY-XVNBXDOJSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6CC1=C(N(C(=O)NC1=O)C)C=C(CO)CF
CACTVS 3.370CN1C(=O)NC(=O)C(=C1\C=C(CO)/CF)C
CACTVS 3.370CN1C(=O)NC(=O)C(=C1C=C(CO)CF)C
OpenEye OEToolkits 1.7.6CC1=C(N(C(=O)NC1=O)C)/C=C(/CO)\CF
ACDLabs 12.01O=C1C(=C(\C=C(/CF)CO)N(C(=O)N1)C)C
FormulaC10 H13 F N2 O3
Name6-[(1Z)-3-fluoro-2-(hydroxymethyl)prop-1-en-1-yl]-1,5-dimethylpyrimidine-2,4(1H,3H)-dione
ChEMBL
DrugBank
ZINCZINC000098208901
PDB chain4jby Chain B Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4jby Synthesis, crystal structure, and in vitro biological evaluation of C-6 pyrimidine derivatives: new lead structures for monitoring gene expression in vivo.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		W88 I97 Q125 M128 R163 A168 Y172 R222
Binding residue
(residue number reindexed from 1)		W43 I52 Q80 M83 R113 A118 Y122 R172
Annotation score1
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 D112 R113 R170 R172 E175
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:4jby, PDBe:4jby, PDBj:4jby
PDBsum4jby
PubMed
UniProtP0DTH5|KITH_HHV11 Thymidine kinase (Gene Name=TK)

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