Structure of PDB 7cl6 Chain F Binding Site BS01

Receptor Information
>7cl6 Chain F (length=275) Species: 1967 (Streptomyces kanamyceticus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HMALAAPPGELTLALTPDDKTLDPASLDRALAILAEHGILVLTGMLRTRL
TDQLRTAMLDDLPEVLRQQDVPTNFVPGHVQQDPPVRESLLFPDVLLNPV
VYQITHAVLGADARNAVYSGNMNLPGSHEQPVHLDEPHLWPGISHPPYCL
CVDVPLIDFTLENGSTEYWPGSHVLNPDECYDERGCVLPAELERRRAVAP
PVRFPIPVGSVVIRDGRLWHRGVPNLSAAPRPLLAMTHYTEWFDMPPIQL
PDTVKSWVDGSDRHTHAHFVHPFAV
Ligand information
Ligand IDXXX
InChIInChI=1S/C12H26N4O6/c13-2-5-8(18)9(19)6(16)12(21-5)22-11-4(15)1-3(14)7(17)10(11)20/h3-12,17-20H,1-2,13-16H2/t3-,4+,5-,6-,7+,8-,9-,10-,11-,12-/m1/s1
InChIKeySYJXFKPQNSDJLI-HKEUSBCWSA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC[CH]1O[CH](O[CH]2[CH](N)C[CH](N)[CH](O)[CH]2O)[CH](N)[CH](O)[CH]1O
OpenEye OEToolkits 1.5.0C1C(C(C(C(C1N)OC2C(C(C(C(O2)CN)O)O)N)O)O)N
CACTVS 3.341NC[C@H]1O[C@H](O[C@@H]2[C@@H](N)C[C@@H](N)[C@H](O)[C@H]2O)[C@H](N)[C@@H](O)[C@@H]1O
ACDLabs 10.04O(C1C(O)C(O)C(N)CC1N)C2OC(C(O)C(O)C2N)CN
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)N)O)O)N
FormulaC12 H26 N4 O6
Name(1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2,6-diamino-2,6-dideoxy-alpha-D-glucopyranoside;
(2R,3S,4R,5R,6R)-6-((1R,2R,3S,4R,6S)-4,6-DIAMINO-2,3-DIHYDROXYCYCLOHEXYLOXY)-5-AMINO-2-(AMINOMETHYL)-TETRAHYDRO-2H-PYRA N-3,4-DIOL;
NEOMYCIN A;
NEAMINE;
(1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2,6-diamino-2,6-dideoxy-alpha-D-glucoside;
(1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2,6-diamino-2,6-dideoxy-D-glucoside;
(1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2,6-diamino-2,6-dideoxy-glucoside
ChEMBLCHEMBL427409
DrugBankDB04808
ZINCZINC000004095654
PDB chain7cl6 Chain F Residue 303 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB7cl6 Stepwise Post-glycosylation Modification of Sugar Moieties in Kanamycin Biosynthesis.
Resolution2.44 Å
Binding residue
(original residue number in PDB)
N73 Q80 N120 D134 E135 F282
Binding residue
(residue number reindexed from 1)
N74 Q81 N121 D135 E136 F273
Annotation score3
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

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Molecular Function

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Biological Process
External links
PDB RCSB:7cl6, PDBe:7cl6, PDBj:7cl6
PDBsum7cl6
PubMed33403742
UniProtQ6L732|KANJ_STRKN Kanamycin B dioxygenase (Gene Name=kanJ)

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