Structure of PDB 8rpl Chain D Binding Site BS01

Receptor Information
>8rpl Chain D (length=626) Species: 2026724 (Chloroflexota bacterium) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LIEERLFPPPEDIVKNANITAYMKSKGFDDYEAFYRWSLANRFEFWNDMA
KELHWFEPWKSTFEWTDKPFFKWFTDGKFNIAYNCLDRYMGTPIEDKVAF
YWEGDDGSSRAYTYKEMYVLTNRVAKVLQNQGVKKGDRVAIYMPMIPEMA
ASVLACARLGAPHMVVFGGFAASSLRDRMNDCDAKVLITADGGYRGGKVI
ELKKIADEAVAETPTIEKVFVQRHTGFEVPMAEGRDVYLDVLLNDIPEDT
VVPCEPVDSEDMLYILYTSGSTGKPKGVVHVHGGYAVGCYATTKFVFDIK
PSDVFWCTADIGWVTGHSYTIYGPMMNAASIVLFEGIPTYPAADRFWSIV
EKYKVNIIYTAPTAIRSLMRFGEELPARHDLSSLRILGTVGEPINPEAWM
WYRKNIGHNELPIMDTWWQTETGMILISPTPILPLKPGSASRPLPTIEAD
VVNKDGKPVGPEHGGFLIIRHPWPAQMRTIFGDPDRYKTYWETIPDVYFA
GDAATMDKMGYFRIQGRVDDVIKVSGHRLGSMEIESSLVSHPAVAEAAAI
GKPDEVKGEHVKVFVILRNGVEPTESLAVELKRHVRTLVGPLATPDELEF
VTSLPKTRSGKIMRRVVRARELGEPV
Ligand information
Ligand ID6R9
InChIInChI=1S/C12H16N5O8P/c1-5(18)25-26(21,22)23-2-6-8(19)9(20)12(24-6)17-4-16-7-10(13)14-3-15-11(7)17/h3-4,6,8-9,12,19-20H,2H2,1H3,(H,21,22)(H2,13,14,15)/t6-,8-,9-,12-/m1/s1
InChIKeyUBPVOHPZRZIJHM-WOUKDFQISA-N
SMILES
SoftwareSMILES
CACTVS 3.385CC(=O)O[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
OpenEye OEToolkits 2.0.5CC(=O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)O
CACTVS 3.385CC(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
OpenEye OEToolkits 2.0.5CC(=O)OP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O
FormulaC12 H16 N5 O8 P
Name[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] ethanoate
ChEMBL
DrugBank
ZINCZINC000004096994
PDB chain8rpl 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

[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]
PDB8rpl Acetyl-CoA synthetase activity is enzymatically regulated by lysine acetylation using acetyl-CoA or acetyl-phosphate as donor molecule.
Resolution2.37 Å
Binding residue
(original residue number in PDB)		G404 E405 P406 T429 W430 W431 Q432 T433 D515 R530 K536 R541
Binding residue
(residue number reindexed from 1)		G391 E392 P393 T416 W417 W418 Q419 T420 D502 R517 K523 R528
Annotation score3
Gene Ontology
Molecular Function
GO:0003987 acetate-CoA ligase activity
GO:0005524 ATP binding
GO:0016874 ligase activity
Biological Process
GO:0006085 acetyl-CoA biosynthetic process
GO:0019427 acetyl-CoA biosynthetic process from acetate
Cellular Component
GO:0005829 cytosol

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8rpl, PDBe:8rpl, PDBj:8rpl
PDBsum8rpl
PubMed39019872
UniProtA0A535FEC2

[Back to BioLiP]