Structure of PDB 3ik1 Chain A Binding Site BS01

Receptor Information
>3ik1 Chain A (length=311) Species: 1582 (Lacticaseibacillus casei) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MLEQPYLDLAKKVLDEGHFKPDRTHTGTYSIFGHQMRFDLSKGFPLLTTK
KVPFGLIKSELLWFLHGDTNIRFLLQHRNHIWDEWAFEKWVKSDEYHGPD
MTDFGHRSQKDPEFAAVYHEEMAKFDDRVLHDDAFAAKYGDLGLVYGSQW
RAWHTSKGDTIDQLGDVIEQIKTHPYSRRLIVSAWNPEDVPTMALPPCHT
LYQFYVNDGKLSLQLYQRSADIFLGVPFNIASYALLTHLVAHECGLEVGE
FIHTFGDAHLYVNHLDQIKEQLSRTPRPAPTLQLNPDKHDIFDFDMKDIK
LLNYDPYPAIK
Ligand information
Ligand ID20C
InChIInChI=1S/C16H11NO5/c1-8-3-2-4-11-13(8)15(20)17(14(11)19)9-5-6-10(16(21)22)12(18)7-9/h2-7,18H,1H3,(H,21,22)
InChIKeySPKSOWKQTVDRTK-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.352Cc1cccc2C(=O)N(c3ccc(C(O)=O)c(O)c3)C(=O)c12
OpenEye OEToolkits 1.7.0Cc1cccc2c1C(=O)N(C2=O)c3ccc(c(c3)O)C(=O)O
ACDLabs 11.02O=C(O)c1ccc(cc1O)N3C(=O)c2cccc(c2C3=O)C
FormulaC16 H11 N O5
Name2-hydroxy-4-(4-methyl-1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)benzoic acid;
2-hydroxy-4-(4-methyl-1,3-dioxo-2,3-dihydro-1H- isoindol-2-yl)benzoic acid
ChEMBLCHEMBL1229792
DrugBank
ZINCZINC000058631509
PDB chain3ik1 Chain A Residue 490 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3ik1 Identification of the binding modes of N-phenylphthalimides inhibiting bacterial thymidylate synthase through X-ray crystallography screening
Resolution2.25 Å
Binding residue
(original residue number in PDB)		E60 I81 W82 W85 L195
Binding residue
(residue number reindexed from 1)		E60 I81 W82 W85 L195
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=4.85,Ki=14uM
BindingDB: Ki=14000nM
Enzymatic activity
Catalytic site (original residue number in PDB) E60 W82 Y146 C198 R218 D221
Catalytic site (residue number reindexed from 1) E60 W82 Y146 C198 R218 D221
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:3ik1, PDBe:3ik1, PDBj:3ik1
PDBsum3ik1
PubMed21696158
UniProtP00469|TYSY_LACCA Thymidylate synthase (Gene Name=thyA)

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