Structure of PDB 1nd4 Chain A Binding Site BS02

Receptor Information
>1nd4 Chain A (length=255) Species: 573 (Klebsiella pneumoniae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GSPAAWVERLFGYDWAQQTIGCSDAAVFRLSAQGRPVLFVKTDLSGALNE
LQDEAARLSWLATTGVPCAAVLDVVTEAGRDWLLLGEVPGQDLLSSHLAP
AEKVSIMADAMRRLHTLDPATCPFDHQAKHRIERARTRMEAGLVDQDDLD
EEHQGLAPAELFARLKARMPDGEDLVVTHGDACLPNIMVENGRFSGFIDC
GRLGVADRYQDIALATRDIAEELGGEWADRFLVLYGIAAPDSQRIAFYRL
LDEFF
Ligand information
Ligand IDKAN
InChIInChI=1S/C18H36N4O11/c19-2-6-10(25)12(27)13(28)18(30-6)33-16-5(21)1-4(20)15(14(16)29)32-17-11(26)8(22)9(24)7(3-23)31-17/h4-18,23-29H,1-3,19-22H2/t4-,5+,6-,7-,8+,9-,10-,11-,12+,13-,14-,15+,16-,17-,18-/m1/s1
InChIKeySBUJHOSQTJFQJX-NOAMYHISSA-N
SMILES
SoftwareSMILES
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](O)[CH](O)[CH]1O
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](O)[C@@H](O)[C@@H]1O
ACDLabs 10.04O(C2C(O)C(OC1OC(CN)C(O)C(O)C1O)C(N)CC2N)C3OC(C(O)C(N)C3O)CO
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)CN)O)O)O)O)O[C@@H]3[C@@H]([C@H]([C@@H]([C@H](O3)CO)O)N)O)N
OpenEye OEToolkits 1.5.0C1C(C(C(C(C1N)OC2C(C(C(C(O2)CN)O)O)O)O)OC3C(C(C(C(O3)CO)O)N)O)N
FormulaC18 H36 N4 O11
NameKANAMYCIN A
ChEMBLCHEMBL1384
DrugBankDB01172
ZINCZINC000008214590
PDB chain1nd4 Chain A Residue 1300 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1nd4 The crystal structure of aminoglycoside-3'-phosphotransferase-IIa, an enzyme responsible for antibiotic resistance
Resolution2.1 Å
Binding residue
(original residue number in PDB)		D157 D159 E160 D190 R211 R226 E230 D261 E262 F264
Binding residue
(residue number reindexed from 1)		D148 D150 E151 D181 R202 R217 E221 D252 E253 F255
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) K50 D190 N195 D208
Catalytic site (residue number reindexed from 1) K41 D181 N186 D199
Enzyme Commision number 2.7.1.95: kanamycin kinase.
Gene Ontology
Molecular Function
GO:0005524 ATP binding
GO:0008910 kanamycin kinase activity
GO:0016301 kinase activity
GO:0016773 phosphotransferase activity, alcohol group as acceptor
GO:0046872 metal ion binding
Biological Process
GO:0016310 phosphorylation
GO:0046677 response to antibiotic

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:1nd4, PDBe:1nd4, PDBj:1nd4
PDBsum1nd4
PubMed12628253
UniProtP00552|KKA2_KLEPN Aminoglycoside 3'-phosphotransferase (Gene Name=neo)

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