Structure of PDB 7cl5 Chain E Binding Site BS01

Receptor Information
>7cl5 Chain E (length=279) Species: 1967 (Streptomyces kanamyceticus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LAAPPGELTLALTPDDKTLDPASLDRALAILAEHGILVLTGMLRTRLTDQ
LRTAMLDDLPEVLRQQDVPTNFVPGHVQQDPPVRESLLFPDVLLNPVVYQ
ITHAVLGADARNAVYSGNMNLPGSHEQPVHLDEPHLWPGISHPPYCLCVD
VPLIDFTLENGSTEYWPGSHVLNPDECYDERGCVLPAELERRRAVAPPVR
FPIPVGSVVIRDGRLWHRGVPNLSAAPRPLLAMTHYTEWFDMPPIQLPDT
VKSWVDGSDRHTHAHFVAGDVDHLHPFAV
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 chain7cl5 Chain E Residue 303 [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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PDB7cl5 Stepwise Post-glycosylation Modification of Sugar Moieties in Kanamycin Biosynthesis.
Resolution2.5 Å
Binding residue
(original residue number in PDB)
N73 Q80 N120 D134 E135 R183 G184 F282
Binding residue
(residue number reindexed from 1)
N71 Q78 N118 D132 E133 R181 G182 F277
Annotation score5
Enzymatic activity
Enzyme Commision number 1.14.11.37: kanamycin B dioxygenase.
Gene Ontology
Molecular Function
GO:0016491 oxidoreductase activity
GO:0016706 2-oxoglutarate-dependent dioxygenase activity
Biological Process
GO:0017000 antibiotic biosynthetic process
GO:1901133 kanamycin biosynthetic process

View graph for
Molecular Function

View graph for
Biological Process
External links
PDB RCSB:7cl5, PDBe:7cl5, PDBj:7cl5
PDBsum7cl5
PubMed33403742
UniProtQ6L732|KANJ_STRKN Kanamycin B dioxygenase (Gene Name=kanJ)

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