Structure of PDB 6s0v Chain E Binding Site BS01

Receptor Information
>6s0v Chain E (length=271) 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
VKSWVDGSDRHTHAHFVAGDV
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 chain6s0v Chain E Residue 305 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6s0v A study on the structure, mechanism, and biochemistry of kanamycin B dioxygenase (KanJ)-an enzyme with a broad range of substrates.
Resolution3.0 Å
Binding residue
(original residue number in PDB)
N73 Q80 V116 N120 D134 E135 C150
Binding residue
(residue number reindexed from 1)
N71 Q78 V114 N118 D132 E133 C148
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:6s0v, PDBe:6s0v, PDBj:6s0v
PDBsum6s0v
PubMed32592631
UniProtQ6L732|KANJ_STRKN Kanamycin B dioxygenase (Gene Name=kanJ)

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