Structure of PDB 4pdk Chain A Binding Site BS04

Receptor Information
>4pdk Chain A (length=259) Species: 243277 (Vibrio cholerae O1 biovar El Tor str. N16961) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PAGFAEKYIIESIWNGRFPPGSILPAERELSELIGVTRTTLREVLQRLAR
DGWLTIQHGKPTKVNQFMETSGLHILDTLMTLDAENATSIVEDLLAARTN
ISPIFMRYAFKLNKESAERIMINVIESCEALVNAPSWDAFIAASPYAEKI
QQHVKEDSEKDELKRQEILIAKTFNFYDYMLFQRLAFHSGNQIYGLIFNG
LKKLYDRVGSYYFSNPQARELAMEFYRQLLAVCQSGEREHLPQVIRQYGI
ASGHIWNQM
Ligand information
Ligand ID3VV
InChIInChI=1S/C39H68N7O17P3S/c1-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18-19-30(48)67-23-22-41-29(47)20-21-42-37(51)34(50)39(2,3)25-60-66(57,58)63-65(55,56)59-24-28-33(62-64(52,53)54)32(49)38(61-28)46-27-45-31-35(40)43-26-44-36(31)46/h11-12,26-28,32-34,38,49-50H,4-10,13-25H2,1-3H3,(H,41,47)(H,42,51)(H,55,56)(H,57,58)(H2,40,43,44)(H2,52,53,54)/b12-11-/t28-,32-,33-,34+,38-/m1/s1
InChIKeyXDUHQPOXLUAVEE-BPMMELMSSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CCCCCCCC\C=C/CCCCCCCC(=O)SCCNC(=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
ACDLabs 12.01O=C(SCCNC(=O)CCNC(=O)C(O)C(C)(C)COP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3OP(=O)(O)O)CCCCCCC\C=C/CCCCCCCC
OpenEye OEToolkits 1.9.2CCCCCCCCC=CCCCCCCCC(=O)SCCNC(=O)CCNC(=O)C(C(C)(C)COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)O
OpenEye OEToolkits 1.9.2CCCCCCCC/C=C\CCCCCCCC(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)COP(=O)(O)OP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)O
CACTVS 3.385CCCCCCCCC=CCCCCCCCC(=O)SCCNC(=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
FormulaC39 H68 N7 O17 P3 S
NameS-{(3R,5R,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5-dioxido-10,14-dioxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl} (9Z)-octadec-9-enethioate (non-preferred name);
oleoyl-CoA
ChEMBL
DrugBank
ZINC
PDB chain4pdk Chain B Residue 302 [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]
PDB4pdk The 40-residue insertion in Vibrio cholerae FadR facilitates binding of an additional fatty acyl-CoA ligand.
Resolution2.8 Å
Binding residue
(original residue number in PDB)
P27 M75
Binding residue
(residue number reindexed from 1)
P20 M68
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.22,Kd=6nM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0000062 fatty-acyl-CoA binding
GO:0003677 DNA binding
GO:0003700 DNA-binding transcription factor activity
Biological Process
GO:0006355 regulation of DNA-templated transcription
GO:0006631 fatty acid metabolic process
GO:0019217 regulation of fatty acid metabolic process
GO:0071072 negative regulation of phospholipid biosynthetic process
Cellular Component
GO:0005737 cytoplasm

View graph for
Molecular Function

View graph for
Biological Process

View graph for
Cellular Component
External links
PDB RCSB:4pdk, PDBe:4pdk, PDBj:4pdk
PDBsum4pdk
PubMed25607896
UniProtQ9KQU8|FADR_VIBCH Fatty acid metabolism regulator protein (Gene Name=fadR)

[Back to BioLiP]