Structure of PDB 6nti Chain A Binding Site BS01

Receptor Information
>6nti Chain A (length=268) Species: 543 (Enterobacteriaceae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TPWSKSELVRQLRDLGVRSGDMVMPHVSLRAVGPLADGPQTLVDALIEAV
GPTGNILAFVSWRDSPYEQTLGHDAPPAAIAQSWPAFDPDHAPAYPGFGA
INEFIRTYPGCRRSAHPDASMAAIGPDAAWLVAPHEMGAAYGPRSPIARF
LAHAGKILSIGAGPDAVTALHYAEAVARIEGKRRVTYSMPLLREGKRVWV
TTSDWDSNGILDEYAAPDGPDAVERIARDYLARTRVAQGPVGGAQSRLID
AADIVSFGIEWLEARHAA
Ligand information
Ligand ID9CS
InChIInChI=1S/C18H37N5O10/c19-2-6-11(26)12(27)9(23)17(30-6)32-15-4(20)1-5(21)16(14(15)29)33-18-13(28)8(22)10(25)7(3-24)31-18/h4-18,24-29H,1-3,19-23H2/t4-,5+,6+,7+,8-,9+,10+,11+,12+,13+,14-,15+,16-,17+,18+/m0/s1
InChIKeySKKLOUVUUNMCJE-FQSMHNGLSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C1[C@@H]([C@H]([C@@H]([C@H]([C@@H]1N)O[C@@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CO)O)N)O)O)O[C@@H]3[C@@H]([C@H]([C@@H]([C@H](O3)CN)O)O)N)N
CACTVS 3.341NC[CH]1O[CH](O[CH]2[CH](N)C[CH](N)[CH](O[CH]3O[CH](CO)[CH](O)[CH](N)[CH]3O)[CH]2O)[CH](N)[CH](O)[CH]1O
OpenEye OEToolkits 1.5.0C1C(C(C(C(C1N)OC2C(C(C(C(O2)CO)O)N)O)O)OC3C(C(C(C(O3)CN)O)O)N)N
ACDLabs 10.04O(C2C(O)C(OC1OC(CN)C(O)C(O)C1N)C(N)CC2N)C3OC(C(O)C(N)C3O)CO
CACTVS 3.341NC[C@H]1O[C@H](O[C@@H]2[C@@H](N)C[C@@H](N)[C@H](O[C@H]3O[C@H](CO)[C@@H](O)[C@H](N)[C@H]3O)[C@H]2O)[C@H](N)[C@@H](O)[C@@H]1O
FormulaC18 H37 N5 O10
Name(1R,2S,3S,4R,6S)-4,6-DIAMINO-3-[(3-AMINO-3-DEOXY-ALPHA-D-GLUCOPYRANOSYL)OXY]-2-HYDROXYCYCLOHEXYL 2,6-DIAMINO-2,6-DIDEOXY-ALPHA-D-GLUCOPYRANOSIDE;
Kanamycin B;
Bekanamycin
ChEMBLCHEMBL176
DrugBankDB13673
ZINCZINC000053132258
PDB chain6nti Chain A Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB6nti Low-Barrier and Canonical Hydrogen Bonds Modulate Activity and Specificity of a Catalytic Triad.
Resolution2.3 Å
Binding residue
(original residue number in PDB)
Y85 E86 D136 Y159 D183 H189 S225 N226
Binding residue
(residue number reindexed from 1)
Y67 E68 D118 Y141 D165 H171 S207 N208
Annotation score1
Enzymatic activity
Enzyme Commision number 2.3.1.81: aminoglycoside N(3)-acetyltransferase.
Gene Ontology
Molecular Function
GO:0016746 acyltransferase activity
GO:0046353 aminoglycoside 3-N-acetyltransferase activity
Biological Process
GO:0046677 response to antibiotic

View graph for
Molecular Function

View graph for
Biological Process
External links
PDB RCSB:6nti, PDBe:6nti, PDBj:6nti
PDBsum6nti
PubMed31515870
UniProtC4NV15

[Back to BioLiP]