Structure of PDB 3bnz Chain A Binding Site BS02

Receptor Information
>3bnz Chain A (length=312) Species: 1582 (Lacticaseibacillus casei) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MLEQPYLDLAKKVLDEGHFKPDRTHTGTYSIFGHQMRFDLSKGFPLLTTK
KVPFGLIKSELLWFLHGDTNIRFLLQHRNHIWDEWAFEKWVKSDEYHGDM
TFGHRSQKDPEFAAVYHEEMAKFDDRVLHDDAFAAKYGDLGLVYGSQWRA
WHTSKGDTIDQLGDVIEQIKTHPYSRRLIVSAWNPEDVPTMALPPCHTLY
QFYVNDGKLSLQLYQRSADIFLGVPFNIASYALLTHLVAHECGLEVGEFI
HTFGDAHLYVNHLDQIKEQLSRTPRPAPTLQLNPDKHDIFDFDMKDIKLL
NYDPYPAIKAPV
Ligand information
Ligand IDC16
InChIInChI=1S/C16H10N2O2/c1-10-3-2-4-13-14(10)16(20)18(15(13)19)12-7-5-11(9-17)6-8-12/h2-8H,1H3
InChIKeyMVYDBJXCIFMINH-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0Cc1cccc2c1C(=O)N(C2=O)c3ccc(cc3)C#N
CACTVS 3.341Cc1cccc2C(=O)N(c3ccc(cc3)C#N)C(=O)c12
ACDLabs 10.04N#Cc1ccc(cc1)N3C(=O)c2cccc(c2C3=O)C
FormulaC16 H10 N2 O2
Name4-(4-methyl-1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)benzonitrile
ChEMBLCHEMBL1231557
DrugBankDB07511
ZINCZINC000039046719
PDB chain3bnz Chain A Residue 318 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3bnz Identification of the binding modes of N-phenylphthalimides inhibiting bacterial thymidylate synthase through X-ray crystallography screening
Resolution2.6 Å
Binding residue
(original residue number in PDB)		I81 E84 F228 N229
Binding residue
(residue number reindexed from 1)		I81 E84 F226 N227
Annotation score1
Binding affinityBindingDB: Ki=22000nM
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:3bnz, PDBe:3bnz, PDBj:3bnz
PDBsum3bnz
PubMed21696158
UniProtP00469|TYSY_LACCA Thymidylate synthase (Gene Name=thyA)

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