Structure of PDB 6s0w Chain D Binding Site BS01

Receptor Information
>6s0w Chain D (length=279) Species: 1967 (Streptomyces kanamyceticus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NAMALAAPPGELTLALTPDDKTLDPASLDRALAILAEHGILVLTGMLRTR
LTDQLRTAMLDDLPEVLRQQDVPTNFVPGHVQQDPPVRESLLFPDVLLNP
VVYQITHAVLGADARNAVYSGNMNLPGSHEQPVHLDEPHLWPGISHPPYC
LCVDVPLIDFTLENGSTEYWPGSHVLNPDECYDERGCVLPAELERRRAVA
PPVRFPIPVGSVVIRDGRLWHRGVPNLSAAPRPLLAMTHYTEWFDMPPIQ
LPDTVKSWVDGSDRHTHAHFVAGDVDHLT
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 chain6s0w Chain D Residue 301 [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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PDB6s0w A study on the structure, mechanism, and biochemistry of kanamycin B dioxygenase (KanJ)-an enzyme with a broad range of substrates.
Resolution2.36 Å
Binding residue
(original residue number in PDB)
N73 Q80 N120 D134 E135 R183
Binding residue
(residue number reindexed from 1)
N75 Q82 N122 D136 E137 R185
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:6s0w, PDBe:6s0w, PDBj:6s0w
PDBsum6s0w
PubMed32592631
UniProtQ6L732|KANJ_STRKN Kanamycin B dioxygenase (Gene Name=kanJ)

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