Structure of PDB 2gru Chain A Binding Site BS05

Receptor Information
>2gru Chain A (length=367) Species: 1397 (Niallia circulans) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TTKQICFADRCFNFAFGEHVLESVESYIPRDEFDQYIMISDSGVPDSIVH
YAAEYFGKLAPVHILRFQGGEEYKTLSTVTNLQERAIALGANRRTAIVAV
GGGLTGNVAGVAAGMMFRGIALIHVPTTFLAASDSVLSIKQAVNLTSGKN
LVGFYYPPRFVFADTRILSESPPRQVKAGMCELVKNMLILENDNKEFTED
DLNSANVYSPKQLETFINFCISAKMSVLSEDIYEKKKGLIFEYGHTIGHA
IELAEQGGITHGEAIAVGMIYAAKIANRMNLMPEHDVSAHYWLLNKIGAL
QDIPLKSDPDSIFHYLIHDNKRGYIKLDEDNLGMILLSGVGKPAMYNQTL
LTPVRKTLIKEVIREGL
Ligand information
Ligand IDEXO
InChIInChI=1S/C7H12O4/c1-3-2-4(8)6(10)7(11)5(3)9/h4-11H,1-2H2/t4-,5-,6+,7+/m1/s1
InChIKeyDRZDCPGIBPDBFY-JWXFUTCRSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C=C1C[C@H]([C@@H]([C@H]([C@@H]1O)O)O)O
CACTVS 3.341O[C@@H]1CC(=C)[C@@H](O)[C@H](O)[C@H]1O
ACDLabs 10.04OC1CC(=C)/C(O)C(O)C1O
CACTVS 3.341O[CH]1CC(=C)[CH](O)[CH](O)[CH]1O
OpenEye OEToolkits 1.5.0C=C1CC(C(C(C1O)O)O)O
FormulaC7 H12 O4
Name(1R,2S,3S,4R)-5-METHYLENECYCLOHEXANE-1,2,3,4-TETRAOL
ChEMBL
DrugBank
ZINC
PDB chain2gru Chain A Residue 607 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB2gru Structure of 2-deoxy-scyllo-inosose synthase, a key enzyme in the biosynthesis of 2-deoxystreptamine-containing aminoglycoside antibiotics, in complex with a mechanism-based inhibitor and NAD+
Resolution2.15 Å
Binding residue
(original residue number in PDB)		D135 E183 K186 K225 E235 F242 H246
Binding residue
(residue number reindexed from 1)		D134 E182 K185 K224 E234 F241 H245
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) R119 K141 E183 K225 E235 G239 E243 H246 H250 H262
Catalytic site (residue number reindexed from 1) R118 K140 E182 K224 E234 G238 E242 H245 H249 H261
Enzyme Commision number 4.2.3.124: 2-deoxy-scyllo-inosose synthase.
Gene Ontology
Molecular Function
GO:0003856 3-dehydroquinate synthase activity
GO:0016829 lyase activity
GO:0016838 carbon-oxygen lyase activity, acting on phosphates
GO:0046872 metal ion binding
Biological Process
GO:0009073 aromatic amino acid family biosynthetic process
GO:0017000 antibiotic biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:2gru, PDBe:2gru, PDBj:2gru
PDBsum2gru
PubMed17879343
UniProtQ9S5E2|DOIS_NIACI 2-deoxy-scyllo-inosose synthase (Gene Name=btrC)

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