Structure of PDB 4k4a Chain B Binding Site BS02

Receptor Information
>4k4a Chain B (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 ID0FQ
InChIInChI=1S/C29H42N7O17P3S/c1-29(2,24(40)27(41)32-9-8-20(38)31-10-11-57-13-18(37)17-6-4-3-5-7-17)14-50-56(47,48)53-55(45,46)49-12-19-23(52-54(42,43)44)22(39)28(51-19)36-16-35-21-25(30)33-15-34-26(21)36/h3-7,15-16,19,22-24,28,39-40H,8-14H2,1-2H3,(H,31,38)(H,32,41)(H,45,46)(H,47,48)(H2,30,33,34)(H2,42,43,44)/t19-,22-,23-,24+,28-/m1/s1
InChIKeyWOEFYXMDPBOUAP-VXAHOBLNSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.2CC(C)(COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)C(C(=O)NCCC(=O)NCCSCC(=O)c4ccccc4)O
CACTVS 3.370CC(C)(CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O[P](O)(O)=O)n2cnc3c(N)ncnc23)[CH](O)C(=O)NCCC(=O)NCCSCC(=O)c4ccccc4
CACTVS 3.370CC(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)[C@@H](O)C(=O)NCCC(=O)NCCSCC(=O)c4ccccc4
OpenEye OEToolkits 1.7.2CC(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)[C@H](C(=O)NCCC(=O)NCCSCC(=O)c4ccccc4)O
ACDLabs 12.01O=C(c1ccccc1)CSCCNC(=O)CCNC(=O)C(O)C(C)(C)COP(=O)(O)OP(=O)(O)OCC4OC(n3cnc2c(ncnc23)N)C(O)C4OP(=O)(O)O
FormulaC29 H42 N7 O17 P3 S
Namephenacyl coenzyme A
ChEMBL
DrugBank
ZINCZINC000214185742
PDB chain4k4a Chain B Residue 201 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4k4a Structure and Catalysis in the Escherichia coli Hotdog-fold Thioesterase Paralogs YdiI and YbdB.
Resolution1.89 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=7.8uM
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4k4a, PDBe:4k4a, PDBj:4k4a
PDBsum4k4a
PubMed25010423
UniProtP77781|MENI_ECOLI 1,4-dihydroxy-2-naphthoyl-CoA hydrolase (Gene Name=menI)

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