Structure of PDB 8gri Chain F Binding Site BS03

Receptor Information
>8gri Chain F (length=482) Species: 285500 (Streptomyces luteocolor) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QTDVIVVGNGVLGLSVGVEIARTRPDVRVTLLGKPARQYGATPAAGAMLG
AFGEVTAHALASEHGRKKHALAVQAQRLWPEWIESLEATGTAADGRIKTA
DDTVVLLNTVGHSALDDANFAAVLTALKEANAPHEEIAVESVDWIDPDPN
SRPLRALHIEGEGSVDSGILLAALERSFLQAGGRLHPVDATEIRASHGRV
EGVVTDDGDFLPAGHVVVAAGARSQRLVAALPGLAHRIPRIYDGVGVSAL
VDTWDGSGPATVLRTSNRAFACGLHLVPRAGGSVYIGATNAVCLEPRGAA
SIAETVFLFNCATHQLHRGLNGSELRKVQVGSRPAPIDGFPLIGGTSVEG
LWMLSGTYRDGLHMSPLLARHVVSLMDGGTGVDGLREFRPERDLISAWSR
EEILDDVVRHTMATGYEFPWRLPLEWPHMMETFLQGPFAELADRLSDTYT
PPADLMTAIMFSEREQQDELIAYYADVHREWH
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 F Residue 703 [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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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)
X281 N299 S310 T423 T466 F470
Binding residue
(residue number reindexed from 1)
X272 N290 S301 T414 T457 F461
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

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