Structure of PDB 4ymk Chain D Binding Site BS04

Receptor Information
>4ymk Chain D (length=312) Species: 10090 (Mus musculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DIRPEMKEDIHDPTYQDEEGPPPKLEYVWRNIILMVLLHLGGLYGIILVP
SCKLYTCLFGIFYYMTSALGITAGAHRLWSHRTYKARLPLRIFLIIANTM
AFQNDVYEWARDHRAHHKFSETHADPHNSRRGFFFSHVGWLLVRKHPAVK
EKGGKLDMSDLKAEKLVMFQRRYYKPGLLLMCFILPTLVPWYCWGETFVN
SLFVSTFLRYTLVLNATWLVNSAAHLYGYRPYDKNIQSRENILVSLGAVG
EGFHNYHHTFPFDYSASEYRWHINFTTFFIDCMAALGLAYDRKKVSKATV
LARIKRTGDGSH
Ligand information
Ligand IDMPG
InChIInChI=1S/C21H40O4/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18-25-21(24)20(23)19-22/h9-10,20,22-23H,2-8,11-19H2,1H3/b10-9-/t20-/m1/s1
InChIKeyJPJYKWFFJCWMPK-GDCKJWNLSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CCCCCCCC\C=C/CCCCCCCCOC(=O)[C@H](O)CO
OpenEye OEToolkits 1.7.6CCCCCCCC/C=C\CCCCCCCCOC(=O)[C@@H](CO)O
CACTVS 3.385CCCCCCCCC=CCCCCCCCCOC(=O)[CH](O)CO
OpenEye OEToolkits 1.7.6CCCCCCCCC=CCCCCCCCCOC(=O)C(CO)O
FormulaC21 H40 O4
Name[(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate
ChEMBL
DrugBankDB03831
ZINCZINC000064436846
PDB chain4ymk Chain D Residue 404 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4ymk X-ray structure of a mammalian stearoyl-CoA desaturase.
Resolution2.605 Å
Binding residue
(original residue number in PDB)		C97 G100 I101 Y104 M105 L252 L286
Binding residue
(residue number reindexed from 1)		C57 G60 I61 Y64 M65 L212 L246
Annotation score1
Enzymatic activity
Enzyme Commision number 1.14.19.1: stearoyl-CoA 9-desaturase.
Gene Ontology
Molecular Function
GO:0004768 stearoyl-CoA 9-desaturase activity
GO:0005506 iron ion binding
GO:0016215 acyl-CoA desaturase activity
GO:0016491 oxidoreductase activity
GO:0016717 oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water
GO:0032896 palmitoyl-CoA 9-desaturase activity
GO:0046872 metal ion binding
Biological Process
GO:0006629 lipid metabolic process
GO:0006633 fatty acid biosynthetic process
GO:0006636 unsaturated fatty acid biosynthetic process
GO:0006641 triglyceride metabolic process
GO:0007584 response to nutrient
GO:0008610 lipid biosynthetic process
GO:0009617 response to bacterium
GO:0042632 cholesterol homeostasis
GO:0048733 sebaceous gland development
GO:0050830 defense response to Gram-positive bacterium
GO:0050872 white fat cell differentiation
GO:0050873 brown fat cell differentiation
GO:0055088 lipid homeostasis
GO:0055092 sterol homeostasis
GO:0070542 response to fatty acid
GO:0120162 positive regulation of cold-induced thermogenesis
GO:1903699 tarsal gland development
GO:1903966 monounsaturated fatty acid biosynthetic process
Cellular Component
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0016020 membrane

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4ymk, PDBe:4ymk, PDBj:4ymk
PDBsum4ymk
PubMed26098370
UniProtP13516|ACOD1_MOUSE Acyl-CoA desaturase 1 (Gene Name=Scd1)

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