Structure of PDB 4k2m Chain A Binding Site BS01

Receptor Information
>4k2m Chain A (length=442) Species: 224308 (Bacillus subtilis subsp. subtilis str. 168) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AGMQKQVKISGKSKENMSLLKHLKGDVQGKELVIEDSIVNERWKQVLKEK
IDIEHDLFNYQKNREISKVPFLPVDRLITNDEVEDILNTLTEVLPTGKFT
SGPYLEQFEKVLSTYLHKRYVIATSSGTDAIMIGLLALGLNPGDEVIMPA
NSFSATENAVLASGGVPIYVDINPQTFCIDPDKIEEAITPYTKFILPVHL
YGKHSDMQHIRQIANRYKLKVIEDACQGIGLTDLGKYADITTLSFNPYKN
FGVCGKAGAIATDNEELAKKCIQFSYHGFEVNVKNKKVINFGFNSKMDNL
QAAIGLERMKYLSLNNFKRLFLADRYITQLAELQNKGYIELPELSEDHVW
HLFPIKVRTEDRADIMTKLNEDFGVQTDVYYPILSHMQKTPLVQDKYAGL
QLVHTEKAHSQVLHLPLYPSFTLEEQDRVMEGLFHVIKQEIG
Ligand information
Ligand IDO1G
InChIInChI=1S/C14H22N2O13P2/c1-6-11(17)8(7(2-15-6)4-27-30(21,22)23)3-16-10-12(18)9(5-28-31(24,25)26)29-14(20)13(10)19/h2-3,9-10,12-14,17-20H,4-5H2,1H3,(H2,21,22,23)(H2,24,25,26)/b16-3+/t9-,10+,12-,13-,14+/m1/s1
InChIKeyQZSIYKBKRPMGJB-ZKLPQXMUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6Cc1c(c(c(cn1)COP(=O)(O)O)C=NC2C(C(OC(C2O)O)COP(=O)(O)O)O)O
OpenEye OEToolkits 1.7.6Cc1c(c(c(cn1)COP(=O)(O)O)/C=N/[C@H]2[C@@H]([C@H](O[C@@H]([C@@H]2O)O)COP(=O)(O)O)O)O
CACTVS 3.370Cc1ncc(CO[P](O)(O)=O)c(C=N[CH]2[CH](O)[CH](O)O[CH](CO[P](O)(O)=O)[CH]2O)c1O
CACTVS 3.370Cc1ncc(CO[P](O)(O)=O)c(C=N[C@@H]2[C@@H](O)[C@@H](O)O[C@H](CO[P](O)(O)=O)[C@H]2O)c1O
ACDLabs 12.01O=P(O)(O)OCc1cnc(c(O)c1/C=N/C2C(O)C(OC(O)C2O)COP(=O)(O)O)C
FormulaC14 H22 N2 O13 P2
Name3-deoxy-3-[(E)-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)amino]-6-O-phosphono-alpha-D-gluco pyranose;
3-deoxy-3-[(E)-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)amino]-6-O-phosphono-alpha-D-gluco se;
3-deoxy-3-[(E)-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)amino]-6-O-phosphono-D-glucose;
3-deoxy-3-[(E)-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)amino]-6-O-phosphono-glucose
ChEMBL
DrugBank
ZINCZINC000098209310
PDB chain4k2m Chain A Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4k2m The Structure of NtdA, a Sugar Aminotransferase Involved in the Kanosamine Biosynthetic Pathway in Bacillus subtilis, Reveals a New Subclass of Aminotransferases.
Resolution1.71 Å
Binding residue
(original residue number in PDB)		G125 T126 F151 A153 D222 C224 Q225 S242 N244 Y246 K247 Y379
Binding residue
(residue number reindexed from 1)		G127 T128 F153 A155 D224 C226 Q227 S244 N246 Y248 K249 Y381
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) F151 D222 Q225 N244 K247 K284 K294
Catalytic site (residue number reindexed from 1) F153 D224 Q227 N246 K249 K286 K296
Enzyme Commision number 2.6.1.104: 3-dehydro-glucose-6-phosphate--glutamate transaminase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0008483 transaminase activity
GO:0030170 pyridoxal phosphate binding
Biological Process
GO:0000271 polysaccharide biosynthetic process
GO:0017000 antibiotic biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4k2m, PDBe:4k2m, PDBj:4k2m
PDBsum4k2m
PubMed24097983
UniProtO07566|NTDA_BACSU 3-oxo-glucose-6-phosphate:glutamate aminotransferase (Gene Name=ntdA)

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