Structure of PDB 1p75 Chain D Binding Site BS01

Receptor Information
>1p75 Chain D (length=328) Species: 10331 (Equid alphaherpesvirus 4) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SHMVTIVRIYLDGVYGIGKSTTGRVMASAASGGSPTLYFPEPMAYWRTLF
ETDVISGIYDTQNRKQQGNLAVDDAALITAHYQSRFTTPYLILHDHTCTL
FGGNSLQRGTQPDLTLVFDRHPVASTVCFPAARYLLGDMSMCALMAMVAT
LPREPQGGNIVVTTLNVEEHIRRLRGEQIDITLIATLRNVYFMLVNTCHF
LRSGRVWRDGWGELPTSCGAYKHRATQMDAFQERVSPELGDTLFALFKTQ
ELLDDRGVILEVHAWALDALMLKLRNLNVFSADLSGTPRQCAAVVESLLP
LMSSTLSDFDSASALERAARTFNAEMGV
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 D Residue 504 [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 M62 Y78 Q102 F105 S144 F148 R192 G310 T311 P312
Binding residue
(residue number reindexed from 1)		Y15 G16 I17 G18 K19 S20 T21 E41 M43 Y59 Q83 F86 S125 F129 R173 G286 T287 P288
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) K38 E60 D138 R139 E201
Catalytic site (residue number reindexed from 1) K19 E41 D119 R120 E177
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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