Structure of PDB 3ii4 Chain B Binding Site BS02

Receptor Information
>3ii4 Chain B (length=464) Species: 1773 (Mycobacterium tuberculosis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MTHYDVVVLGAGPGGYVAAIRAAQLGLSTAIVEPKYWGGVCLNVGCIPSK
ALLRNAELVHIFTKDAKAFGISGEVTFDYGIAYDRSRKVAEGRVAGVHFL
MKKNKITEIHGYGTFADANTLLVDLNDGGTESVTFDNAIIATGSSTRLVP
GTSLSANVVTYEEQILSRELPKSIIIAGAGAIGMEFGYVLKNYGVDVTIV
EFLPRALPNEDADVSKEIEKQFKKLGVTILTATKVESIADGGSQVTVTVT
KDGVAQELKAEKVLQAIGFAPNVEGYGLDKAGVALTDRKAIGVDDYMRTN
VGHIYAIGDVNGLLQLAHVAEAQGVVAAETIAGAETLTLGDHRMLPRATF
CQPNVASFGLTEQQARNEGYDVVVAKFPFTANAKAHGVGDPSGFVKLVAD
AKHGELLGGHLVGHDVAELLPELTLAQRWDLTASELARNVHTHPTMSEAL
QECFHGLVGHMINF
Ligand information
Ligand ID3II
InChIInChI=1S/C32H34Cl2N4O5/c1-42-25-10-11-26(28(19-25)43-2)30(40)36-16-13-32(14-17-36)31(41)37(21-38(32)24-6-4-3-5-7-24)20-29(39)35-15-12-22-8-9-23(33)18-27(22)34/h3-11,18-19H,12-17,20-21H2,1-2H3,(H,35,39)
InChIKeyTWOVSEVREOPZGM-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.352COc1ccc(C(=O)N2CCC3(CC2)N(CN(CC(=O)NCCc4ccc(Cl)cc4Cl)C3=O)c5ccccc5)c(OC)c1
OpenEye OEToolkits 1.7.0COc1ccc(c(c1)OC)C(=O)N2CCC3(CC2)C(=O)N(CN3c4ccccc4)CC(=O)NCCc5ccc(cc5Cl)Cl
ACDLabs 11.02Clc1ccc(c(Cl)c1)CCNC(=O)CN3C(=O)C5(N(c2ccccc2)C3)CCN(C(=O)c4ccc(OC)cc4OC)CC5
FormulaC32 H34 Cl2 N4 O5
NameN-[2-(2,4-dichlorophenyl)ethyl]-2-{8-[(2,4-dimethoxyphenyl)carbonyl]-4-oxo-1-phenyl-1,3,8-triazaspiro[4.5]dec-3-yl}acetamide
ChEMBL
DrugBank
ZINCZINC000058638552
PDB chain3ii4 Chain B Residue 465 [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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PDB3ii4 Triazaspirodimethoxybenzoyls as selective inhibitors of mycobacterial lipoamide dehydrogenase .
Resolution2.42 Å
Binding residue
(original residue number in PDB)		A181 I182 E185 N209 P271 R288 G312 L313 L314 Q315 L316 R347 A348
Binding residue
(residue number reindexed from 1)		A181 I182 E185 N209 P271 R288 G312 L313 L314 Q315 L316 R347 A348
Annotation score1
Binding affinityMOAD: Ki=865nM
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) W37 C41 C46 S49 A181 E185 H441 H443 E448
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

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3ii4, PDBe:3ii4, PDBj:3ii4
PDBsum3ii4
PubMed20078138
UniProtP9WHH9|DLDH_MYCTU Dihydrolipoyl dehydrogenase (Gene Name=lpdC)

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