Structure of PDB 6s0v Chain A Binding Site BS01

Receptor Information
>6s0v Chain A (length=282) Species: 1967 (Streptomyces kanamyceticus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ALAAPPGELTLALTPDDKTLDPASLDRALAILAEHGILVLTGMLRTRLTD
QLRTAMLDDLPEVLRQQDVPTNFVPGHVQQDPPVRESLLFPDVLLNPVVY
QITHAVLGADARNAVYSGNMNLPGSHEQPVHLDEPHLWPGISHPPYCLCV
DVPLIDFTLENGSTEYWPGSHVLNPDECYDERGCVLPAELERRRAVAPPV
RFPIPVGSVVIRDGRLWHRGVPNLSAAPRPLLAMTHYTEWFDMPPIQLPD
TVKSWVDGSDRHTHAHFVAGDVDHLTGDHPFA
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 A 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)
N120 D134 C150 T236
Binding residue
(residue number reindexed from 1)
N119 D133 C149 T235
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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