Structure of PDB 8sgr Chain C Binding Site BS02

Receptor Information
>8sgr Chain C (length=393) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SLLPVDDAINGLSEEQRQLRQTMAKFLQEHLAPKAQEIDRSNEFKNLREF
WKQLGNLGVLGITAPVQYGGSGLGYLEHVLVMEEISRASGAVGLSYGAHS
NLCINQLVRNGNEAQKEKYLPKLISGEYIGALAMSEPNAGSDVVSMKLKA
EKKGNHYILNGNKFWITNGPDADVLIVYAKTDLAAVPASRGITAFIVEKG
MPGFSTSKKLDKLGMRGSNTCELIFEDCKIPAANILGHENKGVYVLMSGL
DLERLVLAGGPLGLMQAVLDHTIPYLHVREAFGQKIGHFQLMQGKMADMY
TRLMACRQYVYNVAKACDEGHCTAKDCAGVILYSAECATQVALDGIQCFG
GNGYINDFPMGRFLRDAKLYEIGAGTSEVRRLVIGRAFNADFH
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 chain8sgr Chain D Residue 1101 [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]
PDB8sgr High-Resolution Structural Proteomics of Mitochondria Using the 'Build and Retrieve' Methodology.
Resolution2.84 Å
Binding residue
(original residue number in PDB)		R312 F315 I319 F322 Q380 C381 G384
Binding residue
(residue number reindexed from 1)		R279 F282 I286 F289 Q347 C348 G351
Annotation score3
Enzymatic activity
Enzyme Commision number 1.3.8.1: short-chain acyl-CoA dehydrogenase.
1.3.8.4: isovaleryl-CoA dehydrogenase.
Gene Ontology
Molecular Function
GO:0003995 acyl-CoA dehydrogenase activity
GO:0005515 protein binding
GO:0008470 3-methylbutanoyl-CoA dehydrogenase activity
GO:0016491 oxidoreductase activity
GO:0016627 oxidoreductase activity, acting on the CH-CH group of donors
GO:0016937 short-chain fatty acyl-CoA dehydrogenase activity
GO:0042802 identical protein binding
GO:0050660 flavin adenine dinucleotide binding
Biological Process
GO:0006552 L-leucine catabolic process
GO:0006631 fatty acid metabolic process
GO:0009083 branched-chain amino acid catabolic process
GO:0033539 fatty acid beta-oxidation using acyl-CoA dehydrogenase
Cellular Component
GO:0005654 nucleoplasm
GO:0005739 mitochondrion
GO:0005759 mitochondrial matrix

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8sgr, PDBe:8sgr, PDBj:8sgr
PDBsum8sgr
PubMed37839702
UniProtP26440|IVD_HUMAN Isovaleryl-CoA dehydrogenase, mitochondrial (Gene Name=IVD)

[Back to BioLiP]