Structure of PDB 5h3a Chain B Binding Site BS02

Receptor Information
>5h3a Chain B (length=281) Species: 37296 (Human gammaherpesvirus 8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PHEELQYLRQLREILCRGSDRLTGIGTLSLFGMQARYSLRDHFPLLTTKR
VFWRGVVQELLWFLKGSTDSRELSRTGVKIWDKNGSREFLAGRGLAHRRE
GDLGPVYGFQWRHFGAAYVDADADYTGQGFDQLSYIVDLIKNNPHDRRII
MCAWNPADLSLMALPPCHLLCQFYVADGELSCQLYQRSGDMGLGVPFNIA
SYSLLTYMLAHVTGLRPGEFIHTLGDAHIYKTHIEPLRLQLTRTPRPFPR
LEILRSVSSMEEFTPDDFRLVDYCPHPTIRM
Ligand information
Ligand IDD16
InChIInChI=1S/C21H22N4O6S/c1-11-22-14-4-3-12(9-13(14)19(28)23-11)10-25(2)17-7-6-16(32-17)20(29)24-15(21(30)31)5-8-18(26)27/h3-4,6-7,9,15H,5,8,10H2,1-2H3,(H,24,29)(H,26,27)(H,30,31)(H,22,23,28)/t15-/m0/s1
InChIKeyIVTVGDXNLFLDRM-HNNXBMFYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C(c3sc(N(C)Cc2ccc1NC(=NC(=O)c1c2)C)cc3)NC(C(=O)O)CCC(=O)O
CACTVS 3.370CN(Cc1ccc2NC(=NC(=O)c2c1)C)c3sc(cc3)C(=O)N[CH](CCC(O)=O)C(O)=O
OpenEye OEToolkits 1.7.6CC1=NC(=O)c2cc(ccc2N1)CN(C)c3ccc(s3)C(=O)N[C@@H](CCC(=O)O)C(=O)O
CACTVS 3.370CN(Cc1ccc2NC(=NC(=O)c2c1)C)c3sc(cc3)C(=O)N[C@@H](CCC(O)=O)C(O)=O
OpenEye OEToolkits 1.7.6CC1=NC(=O)c2cc(ccc2N1)CN(C)c3ccc(s3)C(=O)NC(CCC(=O)O)C(=O)O
FormulaC21 H22 N4 O6 S
NameTOMUDEX;
ZD1694;
Raltitrexed
ChEMBLCHEMBL225071
DrugBankDB00293
ZINCZINC000003832372
PDB chain5h3a 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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PDB5h3a Structural Analysis of Thymidylate Synthase from Kaposi's Sarcoma-Associated Herpesvirus with the Anticancer Drug Raltitrexed.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		D242 L245 G246 F249
Binding residue
(residue number reindexed from 1)		D190 L193 G194 F197
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) E111 W133 Y159 C219 R239 D242
Catalytic site (residue number reindexed from 1) E59 W81 Y107 C167 R187 D190
Enzyme Commision number 2.1.1.45: thymidylate synthase.
Gene Ontology
Molecular Function
GO:0004799 thymidylate synthase activity
GO:0016741 transferase activity, transferring one-carbon groups
Biological Process
GO:0006231 dTMP biosynthetic process

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Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5h3a, PDBe:5h3a, PDBj:5h3a
PDBsum5h3a
PubMed27936107
UniProtP90463|TYSY_HHV8P Thymidylate synthase (Gene Name=70)

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