Structure of PDB 4k4b Chain A Binding Site BS04

Receptor Information
>4k4b Chain A (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 C Residue 201 [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)		H106 G108 S109 R110 H111
Binding residue
(residue number reindexed from 1)		H106 G108 S109 R110 H111
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]