Structure of PDB 1p75 Chain A Binding Site BS01

Receptor Information
>1p75 Chain A (length=331) Species: 10331 (Equid alphaherpesvirus 4) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HMVTIVRIYLDGVYGIGKSTTGRVMASAASGGSPTLYFPEPMAYWRTLFE
TDVISGIYDTQNRKQQGNLAVDDAALITAHYQSRFTTPYLILHDHTCTLF
GGNSLQRGTQPDLTLVFDRHPVASTVCFPAARYLLGDMSMCALMAMVATL
PREPQGGNIVVTTLNVEEHIRRLRTRARGEQIDITLIATLRNVYFMLVNT
CHFLRSGRVWRDGWGELPTSCGAYKHRATQMDAFQERVSPELGDTLFALF
KTQELLDDRGVILEVHAWALDALMLKLRNLNVFSADLSGTPRQCAAVVES
LLPLMSSTLSDFDSASALERAARTFNAEMGV
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 chain1p75 Chain A 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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PDB1p75 Structural basis for the dual thymidine and thymidylate kinase activity of herpes thymidine kinases.
Resolution3.02 Å
Binding residue
(original residue number in PDB)		Y34 G35 I36 G37 K38 S39 T40 E60 Y78 Q102 F105 R139 S144 F148 R192 P312
Binding residue
(residue number reindexed from 1)		Y14 G15 I16 G17 K18 S19 T20 E40 Y58 Q82 F85 R119 S124 F128 R172 P291
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) K38 E60 D138 R139 E201
Catalytic site (residue number reindexed from 1) K18 E40 D118 R119 E180
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:1p75, PDBe:1p75, PDBj:1p75
PDBsum1p75
PubMed14527394
UniProtP24425|KITH_EHV4 Thymidine kinase (Gene Name=TK)

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