Structure of PDB 1ebd Chain A Binding Site BS01

Receptor Information
>1ebd Chain A (length=455) Species: 1422 (Geobacillus stearothermophilus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AIETETLVVGAGPGGYVAAIRAAQLGQKVTIVEKGNLGGVCLNVGCIPSK
ALISASHRYEQAKHSEEMGIKAENVTIDFAKVQEWKASVVKKLTGGVEGL
LKGNKVEIVKGEAYFVDANTVRVVNGDSAQTYTFKNAIIATGSRPIELPN
FKFSNRILDSTGALNLGEVPKSLVVIGGGYIGIELGTAYANFGTKVTILE
GAGEILSGFEKQMAAIIKKRLKKKGVEVVTNALAKGAEEREDGVTVTYEA
NGETKTIDADYVLVTVGRRPNTDELGLEQIGIKMTNRGLIEVDQQCRTSV
PNIFAIGDIVPGPALAHKASYEGKVAAEAIAGHPSAVDYVAIPAVVFSDP
ECASVGYFEQQAKDEGIDVIAAKFPFAANGRALALNDTDGFLKLVVRKED
GVIIGAQIIGPNASDMIAELGLAIEAGMTAEDIALTIHAHPTLGEIAMEA
AEVAL
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 chain1ebd Chain A Residue 462 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1ebd Protein-protein interactions in the pyruvate dehydrogenase multienzyme complex: dihydrolipoamide dehydrogenase complexed with the binding domain of dihydrolipoamide acetyltransferase.
Resolution2.6 Å
Binding residue
(original residue number in PDB)		G16 G18 P19 V38 E39 K40 G45 V46 C47 G51 C52 K56 E118 A119 T147 G148 Y186 I187 R274 D314 A320 L321 A322
Binding residue
(residue number reindexed from 1)		G10 G12 P13 V32 E33 K34 G39 V40 C41 G45 C46 K50 E112 A113 T141 G142 Y180 I181 R268 D308 A314 L315 A316
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) P19 L43 C47 C52 S55 N80 V81 Y186 E190 S326 H444 H446 E451
Catalytic site (residue number reindexed from 1) P13 L37 C41 C46 S49 N74 V75 Y180 E184 S320 H438 H440 E445
Enzyme Commision number 1.8.1.4: dihydrolipoyl dehydrogenase.
Gene Ontology
Molecular Function
GO:0004148 dihydrolipoyl dehydrogenase activity
GO:0005515 protein binding
GO:0016491 oxidoreductase activity
GO:0016668 oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor
GO:0050660 flavin adenine dinucleotide binding
Cellular Component
GO:0005737 cytoplasm

View graph for
Molecular Function
View graph for
Cellular Component
External links
PDB RCSB:1ebd, PDBe:1ebd, PDBj:1ebd
PDBsum1ebd
PubMed8805537
UniProtP11959|DLDH1_GEOSE Dihydrolipoyl dehydrogenase (Gene Name=pdhD)

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