Structure of PDB 4g73 Chain A Binding Site BS08

Receptor Information
>4g73 Chain A (length=472) 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
TAQVAHQEAEYLAKNFDKMAQIPNFQKNLSSRKDKIDLLFEENNFKPFKY
NDLGALAYLGSERAIATIRSGKRTFYTGGGLMTFYLWRILYLSMILSARS
RLKVFFDWIKLAFFKRDFFKGL
Ligand information
Ligand IDNAI
InChIInChI=1S/C21H29N7O14P2/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(32)14(30)11(41-21)6-39-44(36,37)42-43(34,35)38-5-10-13(29)15(31)20(40-10)27-3-1-2-9(4-27)18(23)33/h1,3-4,7-8,10-11,13-16,20-21,29-32H,2,5-6H2,(H2,23,33)(H,34,35)(H,36,37)(H2,22,24,25)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyBOPGDPNILDQYTO-NNYOXOHSSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)N5C=CCC(=C5)C(=O)N)O)O)O)O)N
CACTVS 3.341NC(=O)C1=CN(C=CC1)[C@@H]2O[C@H](CO[P@@](O)(=O)O[P@](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)N5C=CCC(=C5)C(=O)N)O)O)O)O)N
CACTVS 3.341NC(=O)C1=CN(C=CC1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
FormulaC21 H29 N7 O14 P2
Name1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE;
NADH
ChEMBLCHEMBL1234616
DrugBankDB00157
ZINCZINC000008215403
PDB chain4g73 Chain A Residue 610 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4g73 Structural insight into the type-II mitochondrial NADH dehydrogenases.
Resolution2.522 Å
Binding residue
(original residue number in PDB)		G235 P238 T239 E272 A273 A305 V306 T339 L447 Y482
Binding residue
(residue number reindexed from 1)		G194 P197 T198 E231 A232 A264 V265 T298 L406 Y441
Annotation score4
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
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4g73, PDBe:4g73, PDBj:4g73
PDBsum4g73
PubMed23086143
UniProtP32340|NDI1_YEAST Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial (Gene Name=NDI1)

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