Structure of PDB 8w7f Chain D Binding Site BS01

Receptor Information
>8w7f Chain D (length=412) Species: 7227 (Drosophila melanogaster) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DYDLVVVGGGIVGAASAREIVLRHPSLKVAVLEKECKLAKHQSGHNSGVI
HAGIYYKPGTLKARLCVEGMHLAYAYLDEKKIPYKKTGKLIVATDEKEVK
LLKDLEKRGIANNVPDLRMIEGSEIQEIEPYCQGVMALHSPHTGIVDWGL
VTEHYGQDFKQCGGDIYLDFNVSKFTETKETDYPVTIHGAKPGQTVRTKN
VLTCGGLQSDLLAEKTGCPRDPRIVPFRGEYLLLTKEKQHMVKGNIYPVP
DPRFPFLGVHFTPRMDGSIWLGPNAVLALKREGYTWGDINLFELFDALRY
PGFVKMASKYIGFGLSEMSKSWFINLQIKALQKYIPDITEYDIQRGPAGV
RAQAMDLDGNLVDDFVFDRGQGSGALAKRVLHCRNAPSPGATSSLAIAKM
IADKIENEFSIG
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 chain8w7f Chain D Residue 502 [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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PDB8w7f Structure and biochemical characterization of L-2-hydroxyglutarate dehydrogenase and its role in the pathogenesis of L-2-hydroxyglutaric aciduria
Resolution2.299 Å
Binding residue
(original residue number in PDB)		G51 I52 V53 E74 K75 H82 Q83 S84 H86 N87 S88 V90 H92 V213 G247 Q250 Y273 R393 P431 G432 A433 T434
Binding residue
(residue number reindexed from 1)		G10 I11 V12 E33 K34 H41 Q42 S43 H45 N46 S47 V49 H51 V172 G205 Q208 Y231 R351 P389 G390 A391 T392
Annotation score1
Enzymatic activity
Enzyme Commision number 1.1.99.2: L-2-hydroxyglutarate dehydrogenase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0003973 (S)-2-hydroxy-acid oxidase activity
GO:0016491 oxidoreductase activity
GO:0016614 oxidoreductase activity, acting on CH-OH group of donors
GO:0047545 2-hydroxyglutarate dehydrogenase activity
GO:0061758 2-hydroxyglutarate dehydrogenase activity, forward reaction
Cellular Component
GO:0005739 mitochondrion

View graph for
Molecular Function
View graph for
Cellular Component
External links
PDB RCSB:8w7f, PDBe:8w7f, PDBj:8w7f
PDBsum8w7f
PubMed37995940
UniProtQ9VJ28

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