Structure of PDB 8gri Chain D Binding Site BS02

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 IDFAD
InChIInChI=1S/C27H33N9O15P2/c1-10-3-12-13(4-11(10)2)35(24-18(32-12)25(42)34-27(43)33-24)5-14(37)19(39)15(38)6-48-52(44,45)51-53(46,47)49-7-16-20(40)21(41)26(50-16)36-9-31-17-22(28)29-8-30-23(17)36/h3-4,8-9,14-16,19-21,26,37-41H,5-7H2,1-2H3,(H,44,45)(H,46,47)(H2,28,29,30)(H,34,42,43)/t14-,15+,16+,19-,20+,21+,26+/m0/s1
InChIKeyVWWQXMAJTJZDQX-UYBVJOGSSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[C@H](O)[C@H](O)[C@H](O)CO[P@](O)(=O)O[P@@](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56)c2cc1C
OpenEye OEToolkits 1.5.0Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)O
OpenEye OEToolkits 1.5.0Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]([C@@H]([C@@H](CO[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)O)O)O
CACTVS 3.341Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[CH](O)[CH](O)[CH](O)CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)c2cc1C
ACDLabs 10.04O=C2C3=Nc1cc(c(cc1N(C3=NC(=O)N2)CC(O)C(O)C(O)COP(=O)(O)OP(=O)(O)OCC6OC(n5cnc4c(ncnc45)N)C(O)C6O)C)C
FormulaC27 H33 N9 O15 P2
NameFLAVIN-ADENINE DINUCLEOTIDE
ChEMBLCHEMBL1232653
DrugBankDB03147
ZINCZINC000008215434
PDB chain8gri Chain D Residue 701 [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)		G17 N18 G19 L21 G42 R46 Q47 A50 T51 A54 M57 D198 A199 A229 G230 R232 G255 G340 R342 T366 Y367 R368 D369 G370 L371 H372
Binding residue
(residue number reindexed from 1)		G5 N6 G7 L9 G30 R34 Q35 A38 T39 A42 M45 D186 A187 A215 G216 R218 G241 G326 R328 T352 Y353 R354 D355 G356 L357 H358
Annotation score4
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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