Structure of PDB 5u0n Chain A Binding Site BS03

Receptor Information
>5u0n Chain A (length=307) Species: 1877 (Micromonospora echinospora) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IVGGSTIQPERVDAAALRQLGDAMRKVVGSADPTPLADLLSGTPVDPDEL
TREVGADGRQALLDSGMAVDDGTTFSSPLRGHQLHGVVVLSDPDVEEEVQ
HRWYVDPLWEADLLIRLMLRRGGARALDMGCGSGVLSLVLADRYESVLGV
DVNPRAVALSRLNAALNGLTNVTFREGDMFEPAEGRFSRIVFNSPTNEEG
NEFVDLLEAGEPILETFFRNVPRKLESGGIVEVNLAMNDYPGDPFRERLA
DWLGLTENGLRVQIFTSQRRATESGGEWKRGWLVVAPGPVGLTEVEWPYH
DRYEEDP
Ligand information
Ligand ID7XP
InChIInChI=1S/C17H34N4O10/c18-4-1-5(19)15(31-17-12(26)8(20)6(23)3-28-17)13(27)14(4)30-16-9(21)11(25)10(24)7(2-22)29-16/h4-17,22-27H,1-3,18-21H2/t4-,5+,6+,7+,8-,9+,10+,11+,12+,13-,14+,15-,16+,17+/m0/s1
InChIKeyRSLPMOUJEPMGIJ-FHNUIXEPSA-N
SMILES
SoftwareSMILES
CACTVS 3.385N[CH]1C[CH](N)[CH](O[CH]2OC[CH](O)[CH](N)[CH]2O)[CH](O)[CH]1O[CH]3O[CH](CO)[CH](O)[CH](O)[CH]3N
ACDLabs 12.01C3(C(O)C(N)C(OC2C(C(OC1C(O)C(C(CO1)O)N)C(CC2N)N)O)OC3CO)O
OpenEye OEToolkits 2.0.6C1[C@@H]([C@H]([C@@H]([C@H]([C@@H]1N)O[C@@H]2[C@@H]([C@H]([C@@H](CO2)O)N)O)O)O[C@@H]3[C@@H]([C@H]([C@@H]([C@H](O3)CO)O)O)N)N
CACTVS 3.385N[C@H]1C[C@@H](N)[C@H](O[C@H]2OC[C@@H](O)[C@H](N)[C@H]2O)[C@@H](O)[C@@H]1O[C@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3N
OpenEye OEToolkits 2.0.6C1C(C(C(C(C1N)OC2C(C(C(CO2)O)N)O)O)OC3C(C(C(C(O3)CO)O)O)N)N
FormulaC17 H34 N4 O10
Name(1R,2S,3S,4R,6S)-4,6-diamino-3-[(3-amino-3-deoxy-alpha-D-xylopyranosyl)oxy]-2-hydroxycyclohexyl 2-amino-2-deoxy-alpha-D-glucopyranoside
ChEMBL
DrugBank
ZINC
PDB chain5u0n Chain A Residue 403 [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]
PDB5u0n Structural Basis of the Selectivity of GenN, an Aminoglycoside N-Methyltransferase Involved in Gentamicin Biosynthesis.
Resolution2.115 Å
Binding residue
(original residue number in PDB)
D95 V96 E97 E98 W110 E111 N194 S195 N198 L208 R281
Binding residue
(residue number reindexed from 1)
D94 V95 E96 E97 W109 E110 N193 S194 N197 L207 R280
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0008168 methyltransferase activity
GO:0008757 S-adenosylmethionine-dependent methyltransferase activity
GO:0046872 metal ion binding
Biological Process
GO:0032259 methylation

View graph for
Molecular Function

View graph for
Biological Process
External links
PDB RCSB:5u0n, PDBe:5u0n, PDBj:5u0n
PDBsum5u0n
PubMed28876898
UniProtQ2MG72

[Back to BioLiP]