Structure of PDB 5yjw Chain A Binding Site BS01

Receptor Information
>5yjw Chain A (length=454) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SGAGPTSFKTMKVIDPSDKPNVLILGSGWGAISFLKHIDTKKYNVSIISP
RSYFLFTPLLPSAPVGTVDEKSIIEPIVNFALKKKGNVTYYEAEATSINP
DRNTVTIKSLSAAEIKYDYLISAVGAEPNTFGIPGVTDYGHFLKEIPNSL
EIRRTFAANLEKANLLPKGDPERRRLLSIVVVGGGPTGVEAAGELQDYVH
QDLRKFLPALAEEVQIHLVEALPIVLNMFEKKLSSYAQSHLENTSIKVHL
RTAVAKVEEKQLLAKTKHEDGKITEETIPYGTLIWATGNKARPVITDLFK
KIPEQNSSKRGLAVNDFLQVKGSNNIFAIGDNAFAGLPPTAQVAHQEAEY
LAKNFDKMAQIPNFQKKIDLLFEENNFKPFKYNDLGALAYLGSERAIATI
RSGKRTFYTGGGLMTFYLWRILYLSMILSARSRLKVFFDWIKLAFFKRDF
FKGL
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 chain5yjw Chain A 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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PDB5yjw Ubiquinone binding site of yeast NADH dehydrogenase revealed by structures binding novel competitive- and mixed-type inhibitors
Resolution1.85 Å
Binding residue
(original residue number in PDB)		G60 S61 G62 W63 G64 S83 P84 R85 T91 P92 E128 A129 A175 V176 G177 L195 T239 R344 G382 D383 P391 T392 A393
Binding residue
(residue number reindexed from 1)		G26 S27 G28 W29 G30 S49 P50 R51 T57 P58 E94 A95 A123 V124 G125 L143 T187 R292 G330 D331 P339 T340 A341
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:5yjw, PDBe:5yjw, PDBj:5yjw
PDBsum5yjw
PubMed29402945
UniProtP32340|NDI1_YEAST Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial (Gene Name=NDI1)

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