Structure of PDB 4k4b Chain F Binding Site BS04

Receptor Information
>4k4b Chain F (length=136) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MIWKRKITLEALNAMGEGNMVGFLDIRFEHIGDDTLEATMPVDSRTKQPF
GLLHGGASVVLAESIGSVAGYLCTEGEQKVVGLEINANHVRSAREGRVRG
VCKPLHLGSRHQVWQIEIFDEKGRLCCSSRLTTAIL
Ligand information
Ligand IDUOQ
InChIInChI=1S/C32H56N7O17P3S/c1-4-5-6-7-8-9-10-11-21(40)17-60-15-14-34-23(41)12-13-35-30(44)27(43)32(2,3)18-53-59(50,51)56-58(48,49)52-16-22-26(55-57(45,46)47)25(42)31(54-22)39-20-38-24-28(33)36-19-37-29(24)39/h19-20,22,25-27,31,42-43H,4-18H2,1-3H3,(H,34,41)(H,35,44)(H,48,49)(H,50,51)(H2,33,36,37)(H2,45,46,47)/t22-,25+,26+,27+,31+/m1/s1
InChIKeyJYQFMIDTWJSOBJ-BDQXTIGLSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.2CCCCCCCCCC(=O)CSCCNC(=O)CCNC(=O)[C@@H](C(C)(C)CO[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]1[C@@H]([C@@H]([C@H](O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)O
OpenEye OEToolkits 1.7.2CCCCCCCCCC(=O)CSCCNC(=O)CCNC(=O)C(C(C)(C)COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)O
CACTVS 3.370CCCCCCCCCC(=O)CSCCNC(=O)CCNC(=O)[CH](O)C(C)(C)CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O[P](O)(O)=O)n2cnc3c(N)ncnc23
ACDLabs 12.01O=C(CCCCCCCCC)CSCCNC(=O)CCNC(=O)C(O)C(C)(C)COP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3OP(=O)(O)O
CACTVS 3.370CCCCCCCCCC(=O)CSCCNC(=O)CCNC(=O)[C@H](O)C(C)(C)CO[P](O)(=O)O[P](O)(=O)OC[C@H]1O[C@@H]([C@@H](O)[C@H]1O[P](O)(O)=O)n2cnc3c(N)ncnc23
FormulaC32 H56 N7 O17 P3 S
Nameundeca-2-one coenzyme A
ChEMBL
DrugBank
ZINCZINC000263620631
PDB chain4k4b Chain H Residue 203 [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]
PDB4k4b Structure and Catalysis in the Escherichia coli Hotdog-fold Thioesterase Paralogs YdiI and YbdB.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		Q48 P49 H54 G55 H89 V90 R91
Binding residue
(residue number reindexed from 1)		Q48 P49 H54 G55 H89 V90 R91
Annotation score3
Binding affinityMOAD: Ki=12.2uM
Enzymatic activity
Enzyme Commision number 3.1.2.28: 1,4-dihydroxy-2-naphthoyl-CoA hydrolase.
Gene Ontology
Molecular Function
GO:0016289 acyl-CoA hydrolase activity
GO:0016787 hydrolase activity
GO:0016790 thiolester hydrolase activity
GO:0061522 1,4-dihydroxy-2-naphthoyl-CoA thioesterase activity
Biological Process
GO:0009234 menaquinone biosynthetic process
Cellular Component
GO:0005829 cytosol

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4k4b, PDBe:4k4b, PDBj:4k4b
PDBsum4k4b
PubMed25010423
UniProtP77781|MENI_ECOLI 1,4-dihydroxy-2-naphthoyl-CoA hydrolase (Gene Name=menI)

[Back to BioLiP]