Structure of PDB 5m4z Chain B Binding Site BS01

Receptor Information
>5m4z Chain B (length=286) Species: 6334 (Trichinella spiralis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
YVNQEELNYLNQLKDIIDHGVRKNDRTGIGTLSTFGTQSRYCLRDDIFPL
LTTKRVFWRGVVEELLWFISGSTNAKQLSEKNVNIWDGNSSREFLDSRGL
YNYEEGDLGPVYGFQWRHFGCPYSSMTADYKGKGYDQLQQCIKMIREEPE
SRRIIMTAWNPCDLEKVALPPCHCFVQFYVADGELSCQMYQRSADMGLGV
PFNIASYSLLTRMIAHITSLKPGFFIHTIGDAHVYLTHVDALKVQMERKP
RPFPKLKILRNVENIDDFRAEDFELINYKPYPKISM
Ligand information
Ligand ID7K8
InChIInChI=1S/C9H16N3O8P/c13-5-3-8(20-6(5)4-19-21(16,17)18)12-2-1-7(11-15)10-9(12)14/h5-6,8,13,15H,1-4H2,(H,10,11,14)(H2,16,17,18)/t5-,6+,8+/m0/s1
InChIKeyBXCKTJBMNGLVHU-SHYZEUOFSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6C\1CN(C(=O)N/C1=N/O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O
OpenEye OEToolkits 2.0.6C1CN(C(=O)NC1=NO)C2CC(C(O2)COP(=O)(O)O)O
CACTVS 3.385ON=C1CCN([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)C(=O)N1
CACTVS 3.385O\N=C\1CCN([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)C(=O)N\1
FormulaC9 H16 N3 O8 P
Name[(2~{R},3~{S},5~{R})-5-[(4~{E})-4-hydroxyimino-2-oxidanylidene-1,3-diazinan-1-yl]-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate
ChEMBL
DrugBank
ZINC
PDB chain5m4z Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5m4z Molecular Mechanism of Thymidylate Synthase Inhibition by N 4 -Hydroxy-dCMP in View of Spectrophotometric and Crystallographic Studies.
Resolution1.179 Å
Binding residue
(original residue number in PDB)
R169 R170
Binding residue
(residue number reindexed from 1)
R152 R153
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) E81 W103 Y129 C189 R209 D212
Catalytic site (residue number reindexed from 1) E64 W86 Y112 C172 R192 D195
Enzyme Commision number 2.1.1.45: thymidylate synthase.
Gene Ontology
Molecular Function
GO:0004799 thymidylate synthase activity
GO:0008168 methyltransferase activity
GO:0016741 transferase activity, transferring one-carbon groups
Biological Process
GO:0006231 dTMP biosynthetic process
GO:0006235 dTTP biosynthetic process
GO:0009165 nucleotide biosynthetic process
GO:0032259 methylation
Cellular Component
GO:0005739 mitochondrion
GO:0005829 cytosol

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Molecular Function

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Biological Process

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Cellular Component
External links
PDB RCSB:5m4z, PDBe:5m4z, PDBj:5m4z
PDBsum5m4z
PubMed33946210
UniProtQ9NDD3

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