Structure of PDB 5z8k Chain B Binding Site BS03

Receptor Information
>5z8k Chain B (length=408) Species: 1877 (Micromonospora echinospora) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KLLAQEPTCPRDADGRPRVFVEGSGAYLTDPDGRRWIDFDNARGSVVLGH
GDEEVAEAIARAARGRSGVGTAWSPVLDSLLGQLQEVCGGDVVGLYRTGT
AALRSVTCAVRDARDRSIVLSSGYHGYDPMWHCDEPFTPNQHGIVEFLFD
LDVLAEWLSRPEQVAAVVISPDHMHLGERWYTEFTRLTKEADVPVIADEV
KVGLRYRAGLSTPLLDPAVWIVAKCLANGSPVAAVGGDAHLLAALEDVSF
TSYFEPTAMAAATTTLRRMATGEPQQAIRAAGDRFIAHTRAAFANAGVPI
DLAGNGNLFQFVCADDEVADAFHAAAAAEGLLFFEGDNQTPSAAFTDEVV
EDACGRIDRVSAALTGRFTDRELTEESWYASAWGAMDGLADRPRTREETT
AIVERLWE
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 chain5z8k Chain B Residue 502 [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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PDB5z8k Complete reconstitution of the diverse pathways of gentamicin B biosynthesis.
Resolution1.759 Å
Binding residue
(original residue number in PDB)
T16 Y132 K209 K232 F342 D345 N346 D395
Binding residue
(residue number reindexed from 1)
T8 Y124 K201 K224 F334 D337 N338 D387
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) Y132 D206 K232
Catalytic site (residue number reindexed from 1) Y124 D198 K224
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0008483 transaminase activity
GO:0030170 pyridoxal phosphate binding
GO:0046872 metal ion binding

View graph for
Molecular Function
External links
PDB RCSB:5z8k, PDBe:5z8k, PDBj:5z8k
PDBsum5z8k
PubMed30643280
UniProtQ70KD9

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