Structure of PDB 5u0t Chain A Binding Site BS02

Receptor Information
>5u0t Chain A (length=311) 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
DRYEEDPDALL
Ligand information
Ligand ID7QM
InChIInChI=1S/C19H39N5O10/c1-24-10-11(26)8(4-25)32-19(14(10)29)34-17-6(22)2-5(21)16(15(17)30)33-18-9(23)13(28)12(27)7(3-20)31-18/h5-19,24-30H,2-4,20-23H2,1H3/t5-,6+,7+,8+,9+,10-,11+,12+,13+,14+,15-,16+,17-,18+,19+/m0/s1
InChIKeyDXFGBSJHOFHYGL-OADJNCRJSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01C3(O)C(OC1C(C(C(CC1N)N)OC2OC(CN)C(C(C2N)O)O)O)OC(CO)C(C3NC)O
OpenEye OEToolkits 2.0.6CNC1C(C(OC(C1O)OC2C(CC(C(C2O)OC3C(C(C(C(O3)CN)O)O)N)N)N)CO)O
OpenEye OEToolkits 2.0.6CN[C@H]1[C@@H]([C@H](O[C@@H]([C@@H]1O)O[C@H]2[C@@H](C[C@@H]([C@H]([C@@H]2O)O[C@@H]3[C@@H]([C@H]([C@@H]([C@H](O3)CN)O)O)N)N)N)CO)O
CACTVS 3.385CN[C@H]1[C@H](O)[C@@H](CO)O[C@H](O[C@H]2[C@H](N)C[C@H](N)[C@@H](O[C@H]3O[C@H](CN)[C@@H](O)[C@H](O)[C@H]3N)[C@@H]2O)[C@@H]1O
CACTVS 3.385CN[CH]1[CH](O)[CH](CO)O[CH](O[CH]2[CH](N)C[CH](N)[CH](O[CH]3O[CH](CN)[CH](O)[CH](O)[CH]3N)[CH]2O)[CH]1O
FormulaC19 H39 N5 O10
Name(1R,2S,3S,4R,6S)-4,6-diamino-3-{[3-deoxy-3-(methylamino)-alpha-D-glucopyranosyl]oxy}-2-hydroxycyclohexyl 2,6-diamino-2,6-dideoxy-alpha-D-glucopyranoside
ChEMBL
DrugBank
ZINC
PDB chain5u0t Chain A Residue 402 [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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PDB5u0t Structural Basis of the Selectivity of GenN, an Aminoglycoside N-Methyltransferase Involved in Gentamicin Biosynthesis.
Resolution2.109 Å
Binding residue
(original residue number in PDB)
D95 V96 E98 W110 E111 N194 S195 N198 L208 E209
Binding residue
(residue number reindexed from 1)
D94 V95 E97 W109 E110 N193 S194 N197 L207 E208
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:5u0t, PDBe:5u0t, PDBj:5u0t
PDBsum5u0t
PubMed28876898
UniProtQ2MG72

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