Structure of PDB 5yjx Chain A Binding Site BS06

Receptor Information
>5yjx Chain A (length=464) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TGVENSGAGPTSFKTMKVIDPQHSDKPNVLILGSGWGAISFLKHIDTKKY
NVSIISPRSYFLFTPLLPSAPVGTVDEKSIIEPIVNFALKKKGNVTYYEA
EATSINPDRNTVTIKSLSAPAEIKYDYLISAVGAEPNTFGIPGVTDYGHF
LKEIPNSLEIRRTFAANLEKANLLPKGDPERRRLLSIVVVGGGPTGVEAA
GELQDYVHQDLRKFLPALAEEVQIHLVEALPIVLNMFEKKLSSYAQSHLE
NTSIKVHLRTAVAKVEEKQLLAKTKHEDGKITEETIPYGTLIWATGNKAR
PVITDLFKKIPEQNSSKRGLAVNDFLQVKGSNNIFAIGDNAFAGLPPTAQ
VAHQEAEYLAKNFDKMAQIPNFQKNDKIDLLFEENNFKPFKYNDLGALAY
LGSERAIATIRSGKRTFYTGGGLMTFYLWRILYLSMILSARSRLKVFFDW
IKLAFFKRDFFKGL
Ligand information
Ligand IDMYX
InChIInChI=1S/C25H33N3O3S2/c1-16(2)9-7-8-10-17(3)24-28-20(15-33-24)25-27-19(14-32-25)11-12-21(30-5)18(4)22(31-6)13-23(26)29/h7-18,21H,1-6H3,(H2,26,29)/b9-7+,10-8+,12-11+,22-13+/t17-,18+,21-/m0/s1
InChIKeyXKTFQMCPGMTBMD-FYHMSGCOSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.5CC(C)C=CC=CC(C)c1nc(cs1)c2nc(cs2)C=CC(C(C)C(=CC(=O)N)OC)OC
CACTVS 3.385CO[C@@H](\C=C\c1csc(n1)c2csc(n2)[C@@H](C)\C=C\C=C\C(C)C)[C@@H](C)C(\OC)=C/C(N)=O
ACDLabs 10.04O=C(N)\C=C(\OC)C(C)C(OC)/C=C/c1nc(sc1)c2nc(sc2)C(\C=C\C=C\C(C)C)C
OpenEye OEToolkits 1.7.5C[C@@H](/C=C/C=C/C(C)C)c1nc(cs1)c2nc(cs2)/C=C/[C@@H]([C@@H](C)/C(=C\C(=O)N)/OC)OC
CACTVS 3.385CO[CH](C=Cc1csc(n1)c2csc(n2)[CH](C)C=CC=CC(C)C)[CH](C)C(OC)=CC(N)=O
FormulaC25 H33 N3 O3 S2
Name(2Z,6E)-7-{2'-[(2E,4E)-1,6-DIMETHYLHEPTA-2,4-DIENYL]-2,4'-BI-1,3-THIAZOL-4-YL}-3,5-DIMETHOXY-4-METHYLHEPTA-2,6-DIENAMID E;
7-[2'-(1,6-DIMETHYL-HEPTA-2,4-DIENYL)-[2,4']BITHIAZOLYL-4-YL]-3,5-DIMETHOXY-4-METHYL-HEPTA-2,6-DIENOIC ACID AMIDE;
MYXOTHIAZOL
ChEMBLCHEMBL454568
DrugBankDB04741
ZINCZINC000012504487
PDB chain5yjx Chain A Residue 607 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5yjx Ubiquinone binding site of yeast NADH dehydrogenase revealed by structures binding novel competitive- and mixed-type inhibitors
Resolution3.21 Å
Binding residue
(original residue number in PDB)		W63 P238 M280 Q394 H397 L447 M485
Binding residue
(residue number reindexed from 1)		W36 P194 M236 Q350 H353 L398 M436
Annotation score1
Enzymatic activity
Enzyme Commision number 1.6.5.9: NADH:ubiquinone reductase (non-electrogenic).
Gene Ontology
Molecular Function
GO:0003954 NADH dehydrogenase activity
GO:0008137 NADH dehydrogenase (ubiquinone) activity
GO:0016491 oxidoreductase activity
GO:0042802 identical protein binding
GO:0050136 NADH:ubiquinone reductase (non-electrogenic) activity
Biological Process
GO:0006116 NADH oxidation
GO:0006120 mitochondrial electron transport, NADH to ubiquinone
GO:0043065 positive regulation of apoptotic process
GO:1902600 proton transmembrane transport
Cellular Component
GO:0005739 mitochondrion
GO:0005743 mitochondrial inner membrane
GO:0005759 mitochondrial matrix

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5yjx, PDBe:5yjx, PDBj:5yjx
PDBsum5yjx
PubMed29402945
UniProtP32340|NDI1_YEAST Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial (Gene Name=NDI1)

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