Structure of PDB 1p7c Chain A Binding Site BS01

Receptor Information
>1p7c Chain A (length=301) Species: 10299 (Human alphaherpesvirus 1 strain 17) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KMPTLLRVYIDGPHGMGKTTTTQLLVALDIVYVPEPRVLGASETIANIYT
TQHRLDQGEISAGDAAVVMTSAQITMGMPYAVTDAVLAPHIGGEAGPPPA
LTLIFDRHPIAALLCYPAARYLMGSMTPQAVLAFVALIPPTLPGTNIVLG
ALPEDRHIDRLAKRQRPGERLDLAMLAAIRRVYGLLANTVRYLQCGGSWR
EDWGQLSGGPRPHIGDTLFTLFRAPELLAPNGDLYNVFAWALDVLAKRLR
SMHVFILDYDQSPAGCRDALLQLTSGMVQTHVTTPGSIPTICDLARTFAR
E
Ligand information
Ligand IDT5A
InChIInChI=1S/C20H30N7O23P5/c1-8-3-26(20(32)25-18(8)31)12-2-9(28)10(45-12)4-43-51(33,34)47-53(37,38)49-55(41,42)50-54(39,40)48-52(35,36)44-5-11-14(29)15(30)19(46-11)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)(H,41,42)(H2,21,22,23)(H,25,31,32)/t9-,10+,11+,12+,14+,15+,19+/m0/s1
InChIKeyJCFDSPQTEMXXLO-SLFMBYJQSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=O)O[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 1.5.0CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)O
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@@](=O)(O)O[P@](=O)(O)O[P@@](=O)(O)O[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)O
CACTVS 3.341CC1=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)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 H30 N7 O23 P5
NameP1-(5'-ADENOSYL)P5-(5'-THYMIDYL)PENTAPHOSPHATE
ChEMBLCHEMBL1236157
DrugBankDB03280
ZINCZINC000169331553
PDB chain1p7c Chain A Residue 503 [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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PDB1p7c Structural basis for the dual thymidine and thymidylate kinase activity of herpes thymidine kinases.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		H58 G59 M60 G61 K62 T64 E83 I97 Y101 Q125 M128 R163 A168 Y172 R216 K219 R220 R222 E225 P333
Binding residue
(residue number reindexed from 1)		H14 G15 M16 G17 K18 T20 E35 I45 Y49 Q73 M76 R107 A112 Y116 R160 K163 R164 R166 E169 P263
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) K18 E35 D106 R107 R164 R166 E169
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:1p7c, PDBe:1p7c, PDBj:1p7c
PDBsum1p7c
PubMed14527394
UniProtP0DTH5|KITH_HHV11 Thymidine kinase (Gene Name=TK)

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