Structure of PDB 6wf2 Chain A Binding Site BS03

Receptor Information
>6wf2 Chain A (length=321) 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
LARIKRTGDGSHKSSENLYFQ
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 chain6wf2 Chain A Residue 403 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6wf2 Structure and Mechanism of a Unique Diiron Center in Mammalian Stearoyl-CoA Desaturase.
Resolution3.51 Å
Binding residue
(original residue number in PDB)
N71 F142 Q143 N144 W149 R151 D152 H153 W180 L181 R184 K185 K190 G193 G194 Y250 T257 V260 N261 A288
Binding residue
(residue number reindexed from 1)
N31 F102 Q103 N104 W109 R111 D112 H113 W140 L141 R144 K145 K150 G153 G154 Y210 T217 V220 N221 A248
Annotation score4
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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Cellular Component
External links
PDB RCSB:6wf2, PDBe:6wf2, PDBj:6wf2
PDBsum6wf2
PubMed32470559
UniProtP13516|ACOD1_MOUSE Acyl-CoA desaturase 1 (Gene Name=Scd1)

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