Structure of PDB 3byx Chain A Binding Site BS01

Receptor Information
>3byx Chain A (length=313) Species: 1582 (Lacticaseibacillus casei) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MLEQPYLDLAKKVLDEGHFKPDRTHTGTYSIFGHQMRFDLSKGFPLLTTK
KVPFGLIKSELLWFLHGDTNIRFLLQHRNHIWDEWAFEKWVKSDEYHGPD
MTDFGHRSQPEFAAVYHEEMAKFDDRVLHDDAFAAKYGDLGLVYGSQWRA
WHTSKGDTIDQLGDVIEQIKTHPYSRRLIVSAWNPEDVPTMALPPCHTLY
QFYVNDGKLSLQLYQRSADIFLGVPFNIASYALLTHLVAHECGLEVGEFI
HTFGDAHLYVNHLDQIKEQLSRTPRPAPTLQLNPDKHDIFDFDMKDIKLL
NYDPYPAIKAPVA
Ligand information
Ligand IDUMP
InChIInChI=1S/C9H13N2O8P/c12-5-3-8(11-2-1-7(13)10-9(11)14)19-6(5)4-18-20(15,16)17/h1-2,5-6,8,12H,3-4H2,(H,10,13,14)(H2,15,16,17)/t5-,6+,8+/m0/s1
InChIKeyJSRLJPSBLDHEIO-SHYZEUOFSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=P(O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)CC2O
CACTVS 3.370O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O
OpenEye OEToolkits 1.7.6C1[C@@H]([C@H](O[C@H]1N2C=CC(=O)NC2=O)COP(=O)(O)O)O
CACTVS 3.370O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O
OpenEye OEToolkits 1.7.6C1C(C(OC1N2C=CC(=O)NC2=O)COP(=O)(O)O)O
FormulaC9 H13 N2 O8 P
Name2'-DEOXYURIDINE 5'-MONOPHOSPHATE;
DUMP
ChEMBLCHEMBL211312
DrugBankDB03800
ZINCZINC000004228260
PDB chain3byx Chain A Residue 317 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3byx Identification of the binding modes of N-phenylphthalimides inhibiting bacterial thymidylate synthase through X-ray crystallography screening
Resolution2.4 Å
Binding residue
(original residue number in PDB)		R23 C198 H199 R218 S219 A220 D221 N229 H259 Y261
Binding residue
(residue number reindexed from 1)		R23 C196 H197 R216 S217 A218 D219 N227 H257 Y259
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) E60 W82 Y146 C198 R218 D221
Catalytic site (residue number reindexed from 1) E60 W82 Y144 C196 R216 D219
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:0005737 cytoplasm
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:3byx, PDBe:3byx, PDBj:3byx
PDBsum3byx
PubMed21696158
UniProtP00469|TYSY_LACCA Thymidylate synthase (Gene Name=thyA)

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