SMTL ID : 3ii4.1

Structure of mycobacterial lipoamide dehydrogenase bound to a triazaspirodimethoxybenzoyl inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.42 Å

Oligo State

homo-dimer

Ligands

2 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.1: 34 residues within 4Å: Chain A: L.11, G.12, G.14, P.15, G.16, V.34, E.35, P.36, Y.38, G.41, V.42, C.43, G.47, C.48, K.52, Y.114, G.115, A.143, T.144, G.145, Y.163, I.184, F.188, Y.278, G.310, D.311, Q.317, L.318, A.319, H.320, A.322 Chain B: H.445, P.446 Ligands: 3II.2 26 PLIP interactions: 25 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.163, A:I.184, A:I.184, A:F.188 Hydrogen bonds: A:G.14, A:G.16, A:G.17, A:Y.38, A:V.42, A:C.43, A:K.52, A:G.115, A:G.115, A:D.311, A:Q.317, A:A.319, A:H.320, A:H.320, B:H.445 Water bridges: A:G.145, A:S.146, A:S.146, A:S.146, A:S.146, A:V.312, A:L.318 FAD.3: 36 residues within 4Å: Chain A: H.445, P.446 Chain B: L.11, G.12, G.14, P.15, G.16, G.17, V.34, E.35, P.36, Y.38, G.41, V.42, C.43, G.47, C.48, K.52, Y.114, G.115, A.143, T.144, G.145, Y.163, I.184, F.188, Y.278, G.310, D.311, Q.317, L.318, A.319, H.320, A.322, F.352 Ligands: 3II.4 25 PLIP interactions: 24 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:V.42, B:Y.163, B:Y.163, B:I.184, B:F.188 Hydrogen bonds: B:G.16, B:G.17, B:Y.38, B:V.42, B:C.43, B:K.52, B:G.115, B:G.115, B:S.146, B:D.311, B:Q.317, B:A.319, B:H.320, B:H.320, A:H.445 Water bridges: B:G.14, B:G.14, B:Y.114, B:G.145, B:V.312

2 x 3II: N-[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(Non-covalent)

3II.2: 21 residues within 4Å: Chain A: K.52, R.149, A.183, I.184, E.187, N.211, E.212, F.271, A.272, P.273, R.290, A.292, G.314, L.315, L.316, Q.317, L.318, R.349, A.350, F.352 Ligands: FAD.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.184, A:N.211, A:R.290, A:L.316 Hydrogen bonds: A:A.183, A:G.314, A:Q.317 Water bridges: A:A.350 3II.4: 18 residues within 4Å: Chain B: K.52, A.183, I.184, E.187, N.211, E.212, P.273, R.290, A.292, G.314, L.315, L.316, Q.317, L.318, R.349, A.350, F.352 Ligands: FAD.3 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:I.184, B:N.211, B:R.290, B:L.316, B:R.349 Hydrogen bonds: B:A.183, B:N.211, B:Q.317, B:Q.317 Water bridges: B:I.184, B:E.212, B:R.290 pi-Cation interactions: B:R.149

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bryk, R. et al., Triazaspirodimethoxybenzoyls as selective inhibitors of mycobacterial lipoamide dehydrogenase . Biochemistry (2010)

Release Date

2010-01-26

Peptides

Dihydrolipoyl dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dihydrolipoyl dehydrogenase

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