Structure of PDB 6rfr Chain E Binding Site BS01

Receptor Information
>6rfr Chain E (length=349) Species: 4952 (Yarrowia lipolytica) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MNSFENLAQDVNITRSGKTLIAKGTGGRSSRTGYTATVFGANGFLGSYLT
AKLAKHGTTVVVPYREEMAKRHLKVTGDLGVVNFLEMDLRNLESIDEAVR
HSDIVVNLIGREYETKNFNYYDVHVEGARRIAEAVKKHNIARYIHVSAFN
AEIDSPSEFNHTKGLGEQVTKDIVPWATIVRPAPMFGREDKWFLDRMARS
PCLVSANKFQETSNPVHVIDVAAALERICFDDSTVAQTFELYGPQKFTQK
QIIDMVSETLRKEVRHIELPKALYQAYTKATQAIWWPTYSPDQVERQFLS
QKIDPSAKTFNDLDLTPMELPDLMFKLIRPYRVNVSQLENKEKTFVHIL
Ligand information
Ligand IDNDP
InChIInChI=1S/C21H30N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1,3-4,7-8,10-11,13-16,20-21,29-31H,2,5-6H2,(H2,23,32)(H,36,37)(H,38,39)(H2,22,24,25)(H2,33,34,35)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyACFIXJIJDZMPPO-NNYOXOHSSA-N
SMILES
SoftwareSMILES
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)OP(=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[P](O)(O)=O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
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[P](O)(O)=O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
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)OP(=O)(O)O)N
FormulaC21 H30 N7 O17 P3
NameNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
ChEMBLCHEMBL407009
DrugBankDB02338
ZINCZINC000008215411
PDB chain6rfr Chain E Residue 401 [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]
PDB6rfr High-resolution cryo-EM structures of respiratory complex I: Mechanism, assembly, and disease.
Resolution3.2 Å
Binding residue
(original residue number in PDB)		G60 G63 F64 L65 R85 L128 I129 G130 R131 F138 A168 F169 K183 M205
Binding residue
(residue number reindexed from 1)		G40 G43 F44 L45 R65 L108 I109 G110 R111 F118 A148 F149 K163 M185
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0044877 protein-containing complex binding
Biological Process
GO:1901006 ubiquinone-6 biosynthetic process
Cellular Component
GO:0005739 mitochondrion

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6rfr, PDBe:6rfr, PDBj:6rfr
PDBsum6rfr
PubMed31844670
UniProtQ6C7X4

[Back to BioLiP]