SMTL ID : 5f04.1

Structure of Transcriptional Regulatory Repressor Protein - EthR from Mycobacterium Tuberculosis in complex with compound 3 at 1.84A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.84 Å

Oligo State

homo-dimer

Ligands

2 x 5TB: 3-cyclopentyl-1-[3-[4-(methylaminomethyl)phenyl]-1,3-diazinan-1-yl]propan-1-one(Non-covalent)

5TB.1: 18 residues within 4Å: Chain A: L.91, W.107, G.110, I.111, F.114, F.118, T.125, Q.129, W.142, M.146, Y.152, T.153, N.180, N.183, E.184, L.187, F.188, W.211 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.91, A:W.107, A:F.114, A:F.114, A:W.142, A:Y.152, A:E.184, A:L.187, A:W.211 Hydrogen bonds: A:N.183 pi-Stacking: A:F.118 5TB.6: 18 residues within 4Å: Chain B: L.91, W.107, G.110, I.111, F.114, F.118, T.125, Q.129, W.142, M.146, Y.152, T.153, N.180, N.183, E.184, L.187, F.188, W.211 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:L.91, B:W.107, B:F.114, B:F.114, B:W.142, B:Y.152, B:E.184, B:L.187, B:W.211 Hydrogen bonds: B:N.183 pi-Stacking: B:F.118

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 2 residues within 4Å: Chain A: D.102, R.103 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.103 Water bridges: A:E.104 Salt bridges: A:R.103 SO4.3: 3 residues within 4Å: Chain A: M.106, W.107, V.156 No protein-ligand interaction detected (PLIP) SO4.7: 2 residues within 4Å: Chain B: D.102, R.103 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.103 Water bridges: B:E.104 Salt bridges: B:R.103 SO4.8: 3 residues within 4Å: Chain B: M.106, W.107, V.156 No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: D.158, R.161, R.168, P.171, A.172 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.161, A:R.168, A:R.168, A:A.172 Water bridges: A:H.173 GOL.9: 5 residues within 4Å: Chain B: D.158, R.161, R.168, P.171, A.172 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.161, B:R.168, B:R.168, B:A.172 Water bridges: B:H.173

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 5 residues within 4Å: Chain A: P.45, L.46, R.126, A.127, A.130 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.46, A:R.126, A:R.126 EDO.10: 5 residues within 4Å: Chain B: P.45, L.46, R.126, A.127, A.130 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.46, B:R.126, B:R.126

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nikiforov, P.O. et al., A fragment merging approach towards the development of small molecule inhibitors of Mycobacterium tuberculosis EthR for use as ethionamide boosters. Org.Biomol.Chem. (2016)

Release Date

2016-02-03

Peptides

HTH-type transcriptional regulator EthR: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

HTH-type transcriptional regulator EthR

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