Structure of PDB 1jeh Chain B Binding Site BS01

Receptor Information

>1jeh Chain B (length=478) Species: 4932 (Saccharomyces cerevisiae)

TINKSHDVVIIGGGPAGYVAAIKAAQLGFNTACVEKRGKLGGTCLNVGCI
PSKALLNNSHLFHQMHTEAQKRGIDVNGDIKINVANFQKAKDDAVKQLTG
GIELLFKKNKVTYYKGNGSFEDETKIRVTPVDGLEGTVKEDHILDVKNII
VATGSEVTPFPGIEIDEEKIVSSTGALSLKEIPKRLTIIGGGIIGLEMGS
VYSRLGSKVTVVEFQPQIGASMDGEVAKATQKFLKKQGLDFKLSTKVISA
KRNDDKNVVEIVVEDTKTNKQENLEAEVLLVAVGRRPYIAGLGAEKIGLE
VDKRGRLVIDDQFNSKFPHIKVVGDVTFGPMLAHKAEEEGIAAVEMLKTG
HGHVNYNNIPSVMYSHPEVAWVGKTEEQLKEAGIDYKIGKFPFAANSRAK
TNQDTEGFVKILIDSKTERILGAHIIGPNAGEMIAEAGLALEYGASAEDV
ARVCHAHPTLSEAFKEANMAAYDKAIHC

Ligand information

• Ligand ID: FAD
• InChI: InChI=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
• InChIKey: VWWQXMAJTJZDQX-UYBVJOGSSA-N
• SMILES:
  CACTVS 3.341: Cc1cc2N=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 1.5.0: Cc1cc2c(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 1.5.0: Cc1cc2c(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 3.341: Cc1cc2N=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 10.04: O=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
• Formula: C27 H33 N9 O15 P2
• Name: FLAVIN-ADENINE DINUCLEOTIDE
• ChEMBL: CHEMBL1232653
• DrugBank: DB03147
• ZINC: ZINC000008215434
• PDB chain: 1jeh Chain B Residue 580

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1jeh Crystal structure of eucaryotic E3, lipoamide dehydrogenase from yeast.
• Resolution: 2.4 Å
• Binding residue (original residue number in PDB): I11 G14 P15 A16 E35 K36 R37 G42 T43 C44 G48 C49 K53 N117 G118 T153 G154 S173 I194 Y288 L292 G324 D325 M331 L332 A333
• Binding residue (residue number reindexed from 1): I11 G14 P15 A16 E35 K36 R37 G42 T43 C44 G48 C49 K53 N117 G118 T153 G154 S173 I194 Y288 L292 G324 D325 M331 L332 A333
• Annotation score: 2

Enzymatic activity

• Catalytic site (original residue number in PDB): L40 C44 C49 S52 I193 E197 T349 H455 H457 E462
• Catalytic site (residue number reindexed from 1): L40 C44 C49 S52 I193 E197 T349 H455 H457 E462
• Enzyme Commision number: 1.8.1.4: dihydrolipoyl dehydrogenase.

Gene Ontology

Molecular Function

• GO:0004148 dihydrolipoyl dehydrogenase activity
• GO:0004375 glycine dehydrogenase (decarboxylating) activity
• GO:0004591 oxoglutarate dehydrogenase (succinyl-transferring) activity
• GO:0004738 pyruvate 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

Biological Process

• GO:0006086 acetyl-CoA biosynthetic process from pyruvate
• GO:0006090 pyruvate metabolic process
• GO:0006099 tricarboxylic acid cycle
• GO:0006103 2-oxoglutarate metabolic process
• GO:0006546 glycine catabolic process
• GO:0006550 isoleucine catabolic process
• GO:0006552 L-leucine catabolic process
• GO:0006564 L-serine biosynthetic process
• GO:0006574 valine catabolic process
• GO:0042743 hydrogen peroxide metabolic process

Cellular Component

• GO:0005739 mitochondrion
• GO:0005759 mitochondrial matrix
• GO:0005960 glycine cleavage complex
• GO:0042645 mitochondrial nucleoid
• GO:0045252 oxoglutarate dehydrogenase complex
• GO:0045254 pyruvate dehydrogenase complex

External links

• PDB: RCSB:1jeh, PDBe:1jeh, PDBj:1jeh
• PDBsum: 1jeh
• PubMed: 9538259
• UniProt: P09624|DLDH_YEAST Dihydrolipoyl dehydrogenase, mitochondrial (Gene Name=LPD1)