Structure of PDB 4k2m Chain B Binding Site BS01

Receptor Information
>4k2m Chain B (length=439) 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]
MQKQVKISGKSKENMSLLKHLKGDVQGKELVIEDSIVNERWKQVLKEKID
IEHDLFNYQKNREISKVPFLPVDRLITNDEVEDILNTLTEVLPTGKFTSG
PYLEQFEKVLSTYLHKRYVIATSSGTDAIMIGLLALGLNPGDEVIMPANS
FSATENAVLASGGVPIYVDINPQTFCIDPDKIEEAITPYTKFILPVHLYG
KHSDMQHIRQIANRYKLKVIEDACQGIGLTDLGKYADITTLSFNPYKNFG
VCGKAGAIATDNEELAKKCIQFSYHGFEVNVKNKKVINFGFNSKMDNLQA
AIGLERMKYLSLNNFKRLFLADRYITQLAELQNKGYIELPELSEDHVWHL
FPIKVRTEDRADIMTKLNEDFGVQTDVYYPILSHMQKTPLVQDKYAGLQL
VHTEKAHSQVLHLPLYPSFTLEEQDRVMEGLFHVIKQEI
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)		T98 S99 Y274 K282 N292
Binding residue
(residue number reindexed from 1)		T98 S99 Y274 K282 N292
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) F151 D222 Q225 N244 K247 K284 K294
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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