Structure of PDB 8gri Chain D Binding Site BS01

Receptor Information
>8gri Chain D (length=477) Species: 285500 (Streptomyces luteocolor) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VIVVGNGVLGLSVGVEIARTRPDVRVTLLGKPARQYGATPAAGAMLGAFG
EVTAHALASEHGRKKHALAVQAQRLWPEWIESLEATGTAADGRIKTADDT
VVLLNTVGHSALDDANFAAVLTALKEANAPHEEIAVESVDWIDPDPNSRP
LRALHIEGEGSVDSGILLAALERSFLQAGGRLHPVDATEIRASHGRVVVT
DDGDFLPAGHVVVAAGARSQRLVAALPGLAHRIPRIYDGVGVSALVDTWD
GSGPATVLRTSNRAFACGLHLVPRAGGSVYIGATNAVCLEPRGAASIAET
VFLFNCATHQLHRGLNGSELRKVQVGSRPAPIDGFPLIGGTSVEGLWMLS
GTYRDGLHMSPLLARHVVSLMDGGTGVDGLREFRPERDLISAWSREEILD
DVVRHTMATGYEFPWRLPLEWPHMMETFLQGPFAELADRLSDTYTPPADL
MTAIMFSEREQQDELIAYYADVHREWH
Ligand information
Ligand IDI55
InChIInChI=1S/C15H25N7O8/c16-1-6(25)19-9-10(26)11(30-14(17)28)5(3-23)29-13(9)22-15-20-7-4(24)2-18-12(27)8(7)21-15/h4-5,7-11,13,23-24,26H,1-3,16H2,(H2,17,28)(H,18,27)(H,19,25)(H2,20,21,22)/t4-,5-,7-,8+,9-,10+,11+,13-/m1/s1
InChIKeyCSLHSYMCGVEZTI-JJYCVBLVSA-N
SMILES
SoftwareSMILES
CACTVS 3.385NCC(=O)N[C@@H]1[C@H](O)[C@@H](OC(N)=O)[C@@H](CO)O[C@H]1N=C2N[C@@H]3[C@H](O)CNC(=O)[C@H]3N2
OpenEye OEToolkits 2.0.7C1C(C2C(C(=O)N1)NC(=NC3C(C(C(C(O3)CO)OC(=O)N)O)NC(=O)CN)N2)O
OpenEye OEToolkits 2.0.7C1[C@H]([C@@H]2[C@@H](C(=O)N1)N/C(=N/[C@H]3[C@@H]([C@@H]([C@H]([C@H](O3)CO)OC(=O)N)O)NC(=O)CN)/N2)O
CACTVS 3.385NCC(=O)N[CH]1[CH](O)[CH](OC(N)=O)[CH](CO)O[CH]1N=C2N[CH]3[CH](O)CNC(=O)[CH]3N2
FormulaC15 H25 N7 O8
Name[(2~{R},3~{R},4~{S},5~{R},6~{R})-6-[(~{E})-[(3~{a}~{S},7~{R},7~{a}~{S})-7-oxidanyl-4-oxidanylidene-3,3~{a},5,6,7,7~{a}-hexahydro-1~{H}-imidazo[4,5-c]pyridin-2-ylidene]amino]-5-(2-azanylethanoylamino)-2-(hydroxymethyl)-4-oxidanyl-oxan-3-yl] carbamate
ChEMBL
DrugBank
ZINC
PDB chain8gri Chain B Residue 703 [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]
PDB8gri N-Formimidoylation/-iminoacetylation modification in aminoglycosides requires FAD-dependent and ligand-protein NOS bridge dual chemistry.
Resolution2.365 Å
Binding residue
(original residue number in PDB)
E434 M438
Binding residue
(residue number reindexed from 1)
E420 M424
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0016491 oxidoreductase activity
Cellular Component
GO:0005737 cytoplasm

View graph for
Molecular Function

View graph for
Cellular Component
External links
PDB RCSB:8gri, PDBe:8gri, PDBj:8gri
PDBsum8gri
PubMed37137912
UniProtA0A125SZC1

[Back to BioLiP]