Structure of PDB 7kmy Chain D Binding Site BS02

Receptor Information

>7kmy Chain D (length=465) Species: 1773 (Mycobacterium tuberculosis)

SMTHYDVVVLGAGPGGYVAAIRAAQLGLSTAIVEPKYWGGVCLNVGCIPS
KALLRNAELVHIFTKDAKAFGISGEVTFDYGIAYDRSRKVAEGRVAGVHF
LMKKNKITEIHGYGTFADANTLLVDLNDGGTESVTFDNAIIATGSSTRLV
PGTSLSANVVTYEEQILSRELPKSIIIAGAGAIGMEFGYVLKNYGVDVTI
VEFLPRALPNEDADVSKEIEKQFKKLGVTILTATKVESIADGGSQVTVTV
TKDGVAQELKAEKVLQAIGFAPNVEGYGLDKAGVALTDRKAIGVDDYMRT
NVGHIYAIGDVNGLLQLAHVAEAQGVVAAETIAGAETLTLGDHRMLPRAT
FCQPNVASFGLTEQQARNEGYDVVVAKFPFTANAKAHGVGDPSGFVKLVA
DAKHGELLGGHLVGHDVAELLPELTLAQRWDLTASELARNVHTHPTMSEA
LQECFHGLVGHMINF

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: 7kmy Chain D Residue 501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7kmy Whole cell active inhibitors of mycobacterial lipoamide dehydrogenase afford selectivity over the human enzyme through tight binding interactions
• Resolution: 2.21 Å
• Binding residue (original residue number in PDB): L9 G10 G12 P13 V32 E33 P34 Y36 V40 C41 G45 C46 K50 Y112 G113 A141 T142 Y161 I182 Y276 G308 D309 Q315 L316 A317
• Binding residue (residue number reindexed from 1): L10 G11 G13 P14 V33 E34 P35 Y37 V41 C42 G46 C47 K51 Y113 G114 A142 T143 Y162 I183 Y277 G309 D310 Q316 L317 A318
• Annotation score: 2

Enzymatic activity

• Catalytic site (original residue number in PDB): W37 C41 C46 S49 A181 E185 H441 H443 E448
• Catalytic site (residue number reindexed from 1): W38 C42 C47 S50 A182 E186 H442 H444 E449
• Enzyme Commision number: 1.8.1.4: dihydrolipoyl dehydrogenase.

Gene Ontology

Molecular Function

• GO:0004148 dihydrolipoyl dehydrogenase activity
• GO:0004591 oxoglutarate dehydrogenase (succinyl-transferring) activity
• GO:0005515 protein binding
• GO:0015036 disulfide oxidoreductase activity
• GO:0016209 antioxidant activity
• GO:0016491 oxidoreductase activity
• GO:0016655 oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor
• GO:0016668 oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor
• GO:0035375 zymogen binding
• GO:0050660 flavin adenine dinucleotide binding
• GO:0070404 NADH binding

Biological Process

• GO:0045454 cell redox homeostasis
• GO:0098869 cellular oxidant detoxification

Cellular Component

• GO:0005576 extracellular region
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005886 plasma membrane
• GO:0045254 pyruvate dehydrogenase complex

External links

• PDB: RCSB:7kmy, PDBe:7kmy, PDBj:7kmy
• PDBsum: 7kmy
• PubMed: 33527832
• UniProt: P9WHH9|DLDH_MYCTU Dihydrolipoyl dehydrogenase (Gene Name=lpdC)