Structure of PDB 6cbm Chain A Binding Site BS02

Receptor Information
>6cbm Chain A (length=409) Species: 1906 (Streptomyces fradiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SLLAEFPTCPRDEKDRPRVFTAASGAWLTDESGFRWIDFDNARGSILLGH
GDPVVAEAVARAATGADGTATGWSRRVDAVLERLHALCGGEVVGLFRSGT
AAVRAAVLAVREATGRPLLLSAGYHGYDPMWYPSEAPLEPNADGVVDFFF
DLGLLRELLRAPERVAAVVVSPDHMHLSPGWYRELRRLCSAAGVVLVADE
VKVGLRYAPGLSTAELLAPDVWVVAKGMANGHAVSAVGGSRRLLKPLKEV
SFTSFFEPTILAAADAALARVATGEPQRAVREAGDRFLRHARKALDDASL
PVEIAGDGTFFQFVPATEELEEALYGAANAEGLLFYAGDNQGVSAAFDEA
VLGEAERRFARVCERLAPYAGGEPVGDAARYRVAWNVMDGLRQAPRDREE
TTGLLARLL
Ligand information
Ligand IDOZY
InChIInChI=1S/C31H56N7O18P/c1-9-19(40)11(10(4-38-9)8-50-57(47,48)49)5-37-6-15-22(43)24(45)18(36)30(52-15)55-27-16(7-39)53-31(25(27)46)56-28-20(41)12(33)2-13(34)26(28)54-29-17(35)23(44)21(42)14(3-32)51-29/h4,12-18,20-31,37,39-46H,2-3,5-8,32-36H2,1H3,(H2,47,48,49)/t12-,13+,14-,15-,16-,17-,18-,20+,21-,22-,23-,24-,25-,26-,27-,28-,29-,30-,31+/m1/s1
InChIKeyXKWYFXMYGMVOPV-AWIIFLAXSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6Cc1c(c(c(cn1)COP(=O)(O)O)CNC[C@@H]2[C@H]([C@@H]([C@H]([C@H](O2)O[C@@H]3[C@H](O[C@H]([C@@H]3O)O[C@@H]4[C@H]([C@@H](C[C@@H]([C@H]4O[C@@H]5[C@@H]([C@H]([C@@H]([C@H](O5)CN)O)O)N)N)N)O)CO)N)O)O)O
CACTVS 3.385Cc1ncc(CO[P](O)(O)=O)c(CNC[C@H]2O[C@H](O[C@H]3[C@@H](O)[C@@H](O[C@@H]3CO)O[C@@H]4[C@@H](O)[C@H](N)C[C@H](N)[C@H]4O[C@H]5O[C@H](CN)[C@@H](O)[C@H](O)[C@H]5N)[C@H](N)[C@@H](O)[C@@H]2O)c1O
OpenEye OEToolkits 2.0.6Cc1c(c(c(cn1)COP(=O)(O)O)CNCC2C(C(C(C(O2)OC3C(OC(C3O)OC4C(C(CC(C4OC5C(C(C(C(O5)CN)O)O)N)N)N)O)CO)N)O)O)O
CACTVS 3.385Cc1ncc(CO[P](O)(O)=O)c(CNC[CH]2O[CH](O[CH]3[CH](O)[CH](O[CH]3CO)O[CH]4[CH](O)[CH](N)C[CH](N)[CH]4O[CH]5O[CH](CN)[CH](O)[CH](O)[CH]5N)[CH](N)[CH](O)[CH]2O)c1O
ACDLabs 12.01O=P(O)(O)OCc1cnc(c(c1CNCC2C(O)C(C(C(O2)OC3C(CO)OC(C3O)OC5C(OC4C(C(C(C(O4)CN)O)O)N)C(N)CC(C5O)N)N)O)O)C
FormulaC31 H56 N7 O18 P
Name
ChEMBL
DrugBank
ZINC
PDB chain6cbm Chain B Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB6cbm The three-dimensional structure of NeoB: An aminotransferase involved in the biosynthesis of neomycin.
Resolution1.65 Å
Binding residue
(original residue number in PDB)		E254 F257 T258
Binding residue
(residue number reindexed from 1)		E249 F252 T253
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) Y129 D204 K231
Catalytic site (residue number reindexed from 1) Y124 D199 K226
Enzyme Commision number 2.6.1.93: neamine transaminase.
2.6.1.95: neomycin C transaminase.
Gene Ontology
Molecular Function
GO:0008483 transaminase activity
GO:0030170 pyridoxal phosphate binding
Biological Process
GO:0009058 biosynthetic process
GO:0017000 antibiotic biosynthetic process
GO:1901158 neomycin biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6cbm, PDBe:6cbm, PDBj:6cbm
PDBsum6cbm
PubMed29516565
UniProtQ53U08|NEON_STRFR Neamine transaminase NeoN (Gene Name=neoN)

[Back to BioLiP]