Structure of PDB 4qn9 Chain A Binding Site BS04

Receptor Information
>4qn9 Chain A (length=321) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SKKGKDGRFVNPWPTWKNPSIPNSSVPSSKEELDKELPVLKPYFITNPEE
AGVREAGLRVTWLGHATVMVEMDELIFLTDPIFSSRASPSQYMGPKRFRR
SPCTISELPPIDAVLISHNHYDHLDYNSVIALNERFGNELRWFVPLGLLD
WMQKCGCENVIELDWWEENCVPGHDKVTFVFTPSQHWCKRTLMDDNKVLW
GSWSVLGPWNRFFFAGDTGYCPAFEEIGKRFGPFDLAAIPIGAYEPRWFM
KYQHVDPEEAVRIHTDVQTKKSMAIHWGTFALANEHYLEPPVKLNEALER
YGLNAEDFFVLKHGESRYLNN
Ligand information
Ligand IDDXC
InChIInChI=1S/C24H40O4/c1-14(4-9-22(27)28)18-7-8-19-17-6-5-15-12-16(25)10-11-23(15,2)20(17)13-21(26)24(18,19)3/h14-21,25-26H,4-13H2,1-3H3,(H,27,28)/t14-,15-,16-,17+,18-,19+,20+,21+,23+,24-/m1/s1
InChIKeyKXGVEGMKQFWNSR-LLQZFEROSA-N
SMILES
SoftwareSMILES
CACTVS 3.341C[CH](CCC(O)=O)[CH]1CC[CH]2[CH]3CC[CH]4C[CH](O)CC[C]4(C)[CH]3C[CH](O)[C]12C
OpenEye OEToolkits 1.5.0C[C@H](CCC(=O)O)[C@H]1CC[C@@H]2[C@@]1([C@H](C[C@H]3[C@H]2CC[C@H]4[C@@]3(CC[C@H](C4)O)C)O)C
OpenEye OEToolkits 1.5.0CC(CCC(=O)O)C1CCC2C1(C(CC3C2CCC4C3(CCC(C4)O)C)O)C
CACTVS 3.341C[C@H](CCC(O)=O)[C@H]1CC[C@H]2[C@@H]3CC[C@@H]4C[C@H](O)CC[C@]4(C)[C@H]3C[C@H](O)[C@]12C
ACDLabs 10.04O=C(O)CCC(C4CCC3C2C(C1(C)CCC(O)CC1CC2)CC(O)C34C)C
FormulaC24 H40 O4
Name(3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID;
DEOXYCHOLIC ACID
ChEMBLCHEMBL406393
DrugBankDB03619
ZINCZINC000003914810
PDB chain4qn9 Chain A Residue 505 [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]
PDB4qn9 Structure of human N-acylphosphatidylethanolamine-hydrolyzing phospholipase D: regulation of fatty acid ethanolamide biosynthesis by bile acids.
Resolution2.652 Å
Binding residue
(original residue number in PDB)		Y159 M160
Binding residue
(residue number reindexed from 1)		Y92 M93
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=4.41,Kd=38.5uM
Enzymatic activity
Enzyme Commision number 3.1.4.54: N-acetylphosphatidylethanolamine-hydrolyzing phospholipase D.
Gene Ontology
Molecular Function
GO:0008270 zinc ion binding
GO:0016787 hydrolase activity
GO:0032052 bile acid binding
GO:0042802 identical protein binding
GO:0046872 metal ion binding
GO:0070290 N-acylphosphatidylethanolamine-specific phospholipase D activity
Biological Process
GO:0001523 retinoid metabolic process
GO:0001659 temperature homeostasis
GO:0009395 phospholipid catabolic process
GO:0048874 host-mediated regulation of intestinal microbiota composition
GO:0050729 positive regulation of inflammatory response
GO:0070291 N-acylethanolamine metabolic process
GO:0070292 N-acylphosphatidylethanolamine metabolic process
GO:0090336 positive regulation of brown fat cell differentiation
Cellular Component
GO:0000139 Golgi membrane
GO:0005634 nucleus
GO:0005635 nuclear envelope
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005768 endosome
GO:0005769 early endosome
GO:0005794 Golgi apparatus
GO:0016020 membrane
GO:0030868 smooth endoplasmic reticulum membrane
GO:0031901 early endosome membrane
GO:0042622 photoreceptor outer segment membrane
GO:0042734 presynaptic membrane
GO:0045211 postsynaptic membrane
GO:0070062 extracellular exosome
GO:0098686 hippocampal mossy fiber to CA3 synapse
GO:0098793 presynapse

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4qn9, PDBe:4qn9, PDBj:4qn9
PDBsum4qn9
PubMed25684574
UniProtQ6IQ20|NAPEP_HUMAN N-acyl-phosphatidylethanolamine-hydrolyzing phospholipase D (Gene Name=NAPEPLD)

[Back to BioLiP]