Structure of PDB 5yjx Chain B Binding Site BS01

Receptor Information
>5yjx Chain B (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 IDFAD
InChIInChI=1S/C27H33N9O15P2/c1-10-3-12-13(4-11(10)2)35(24-18(32-12)25(42)34-27(43)33-24)5-14(37)19(39)15(38)6-48-52(44,45)51-53(46,47)49-7-16-20(40)21(41)26(50-16)36-9-31-17-22(28)29-8-30-23(17)36/h3-4,8-9,14-16,19-21,26,37-41H,5-7H2,1-2H3,(H,44,45)(H,46,47)(H2,28,29,30)(H,34,42,43)/t14-,15+,16+,19-,20+,21+,26+/m0/s1
InChIKeyVWWQXMAJTJZDQX-UYBVJOGSSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[C@H](O)[C@H](O)[C@H](O)CO[P@](O)(=O)O[P@@](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56)c2cc1C
OpenEye OEToolkits 1.5.0Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)O
OpenEye OEToolkits 1.5.0Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]([C@@H]([C@@H](CO[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)O)O)O
CACTVS 3.341Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[CH](O)[CH](O)[CH](O)CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)c2cc1C
ACDLabs 10.04O=C2C3=Nc1cc(c(cc1N(C3=NC(=O)N2)CC(O)C(O)C(O)COP(=O)(O)OP(=O)(O)OCC6OC(n5cnc4c(ncnc45)N)C(O)C6O)C)C
FormulaC27 H33 N9 O15 P2
NameFLAVIN-ADENINE DINUCLEOTIDE
ChEMBLCHEMBL1232653
DrugBankDB03147
ZINCZINC000008215434
PDB chain5yjx Chain B Residue 601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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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)		G60 S61 G62 W63 G64 I82 P84 R85 T91 P92 L94 E128 A129 A175 V176 G177 L195 T239 G382 D383 P391 T392 A393
Binding residue
(residue number reindexed from 1)		G33 S34 G35 W36 G37 I55 P57 R58 T64 P65 L67 E101 A102 A131 V132 G133 L151 T195 G338 D339 P347 T348 A349
Annotation score2
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:5yjx, PDBe:5yjx, PDBj:5yjx
PDBsum5yjx
PubMed29402945
UniProtP32340|NDI1_YEAST Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial (Gene Name=NDI1)

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