Structure of PDB 4g74 Chain B Binding Site BS02

Receptor Information
>4g74 Chain B (length=463) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TMKVIDPQHSDKPNVLILGSGWGAISFLKHIDTKKYNVSIISPRSYFLFT
PLLPSAPVGTVDEKSIIEPIVNFALKKKGNVTYYEAEATSINPDRNTVTI
KSLSAVSQLYQPENHLGLHQAEPAEIKYDYLISAVGAEPNTFGIPGVTDY
GHFLKEIPNSLEIRRTFAANLEKANLLPKGDPERRRLLSIVVVGGGPTGV
EAAGELQDYVHQDLRKFLPALAEEVQIHLVEALPIVLNMFEKKLSSYAQS
HLENTSIKVHLRTAVAKVEEKQLLAKTKHEDGKITEETIPYGTLIWATGN
KARPVITDLFKKIPEQNSSKRGLAVNDFLQVKGSNNIFAIGDNAFAGLPP
TAQVAHQEAEYLAKNFDKMAQIPNFQKNLLFEENNFKPFKYNDLGALAYL
GSERAIATIRSGKRTFYTGGGLMTFYLWRILYLSMILSARSRLKVFFDWI
KLAFFKRDFFKGL
Ligand information
Ligand IDUQ5
InChIInChI=1S/C34H50O4/c1-24(2)14-10-15-25(3)16-11-17-26(4)18-12-19-27(5)20-13-21-28(6)22-23-30-29(7)31(35)33(37-8)34(38-9)32(30)36/h14,16,18,20,22H,10-13,15,17,19,21,23H2,1-9H3/b25-16+,26-18+,27-20+,28-22+
InChIKeyNYFAQDMDAFCWPU-UVCHAVPFSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC1=C(C(=O)C(=C(C1=O)OC)OC)CC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)C
OpenEye OEToolkits 1.5.0CC1=C(C(=O)C(=C(C1=O)OC)OC)C\C=C(/C)\CC\C=C(/C)\CC\C=C(/C)\CC\C=C(/C)\CCC=C(C)C
CACTVS 3.341COC1=C(OC)C(=O)C(=C(C)C1=O)CC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)C
CACTVS 3.341COC1=C(OC)C(=O)C(=C(C)C1=O)C\C=C(/C)CC\C=C(/C)CC\C=C(/C)CC\C=C(/C)CCC=C(C)C
ACDLabs 10.04O=C1C(=C(C(=O)C(OC)=C1OC)C)C\C=C(/C)CC\C=C(/C)CC\C=C(/C)CC\C=C(/C)CC/C=C(/C)C
FormulaC34 H50 O4
Name2,3-DIMETHOXY-5-METHYL-6-(3,11,15,19-TETRAMETHYL-EICOSA-2,6,10,14,18-PENTAENYL)-[1,4]BENZOQUINONE
ChEMBL
DrugBank
ZINCZINC000058649852
PDB chain4g74 Chain B Residue 603 [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]
PDB4g74 Structural insight into the type-II mitochondrial NADH dehydrogenases.
Resolution2.48 Å
Binding residue
(original residue number in PDB)		H397 S484
Binding residue
(residue number reindexed from 1)		H356 S434
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4g74, PDBe:4g74, PDBj:4g74
PDBsum4g74
PubMed23086143
UniProtP32340|NDI1_YEAST Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial (Gene Name=NDI1)

[Back to BioLiP]