Structure of PDB 7kmy Chain D Binding Site BS03

Receptor Information
>7kmy Chain D (length=465) Species: 1773 (Mycobacterium tuberculosis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SMTHYDVVVLGAGPGGYVAAIRAAQLGLSTAIVEPKYWGGVCLNVGCIPS
KALLRNAELVHIFTKDAKAFGISGEVTFDYGIAYDRSRKVAEGRVAGVHF
LMKKNKITEIHGYGTFADANTLLVDLNDGGTESVTFDNAIIATGSSTRLV
PGTSLSANVVTYEEQILSRELPKSIIIAGAGAIGMEFGYVLKNYGVDVTI
VEFLPRALPNEDADVSKEIEKQFKKLGVTILTATKVESIADGGSQVTVTV
TKDGVAQELKAEKVLQAIGFAPNVEGYGLDKAGVALTDRKAIGVDDYMRT
NVGHIYAIGDVNGLLQLAHVAEAQGVVAAETIAGAETLTLGDHRMLPRAT
FCQPNVASFGLTEQQARNEGYDVVVAKFPFTANAKAHGVGDPSGFVKLVA
DAKHGELLGGHLVGHDVAELLPELTLAQRWDLTASELARNVHTHPTMSEA
LQECFHGLVGHMINF
Ligand information
Ligand IDWPM
InChIInChI=1S/C17H19N5O4S/c1-11-6-12-9-18-20-17(12)14(7-11)27(25,26)22(3)10-15(23)19-13-4-5-21(2)16(24)8-13/h4-9H,10H2,1-3H3,(H,18,20)(H,19,23)
InChIKeyPMYKBSXBMRYDGS-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7Cc1cc2cn[nH]c2c(c1)S(=O)(=O)N(C)CC(=O)NC3=CC(=O)N(C=C3)C
CACTVS 3.385CN(CC(=O)NC1=CC(=O)N(C)C=C1)[S](=O)(=O)c2cc(C)cc3cn[nH]c23
ACDLabs 12.01C3(N(C)C=CC(NC(CN(C)S(c2cc(cc1cnnc12)C)(=O)=O)=O)=C3)=O
FormulaC17 H19 N5 O4 S
NameN~2~-methyl-N~2~-[(5-methyl-1H-indazol-7-yl)sulfonyl]-N-(1-methyl-2-oxo-1,2-dihydropyridin-4-yl)glycinamide
ChEMBL
DrugBank
ZINC
PDB chain7kmy 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

[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]
PDB7kmy Whole cell active inhibitors of mycobacterial lipoamide dehydrogenase afford selectivity over the human enzyme through tight binding interactions
Resolution2.21 Å
Binding residue
(original residue number in PDB)
Y16 R93 F99 E321
Binding residue
(residue number reindexed from 1)
Y17 R94 F100 E322
Annotation score1
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

View graph for
Molecular Function

View graph for
Biological Process

View graph for
Cellular Component
External links
PDB RCSB:7kmy, PDBe:7kmy, PDBj:7kmy
PDBsum7kmy
PubMed33527832
UniProtP9WHH9|DLDH_MYCTU Dihydrolipoyl dehydrogenase (Gene Name=lpdC)

[Back to BioLiP]