SMTL ID : 5i7r.1

Mycobacterium tuberculosis CysM in complex with the Urea-scaffold inhibitor 2 [3-(3-([1,1'-biphenyl]-3-yl)ureido)benzoic acid]

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

homo-dimer

Ligands

2 x PLP: PYRIDOXAL-5'-PHOSPHATE(Covalent)

PLP.1: 14 residues within 4Å: Chain A: K.54, N.84, G.185, L.186, G.187, T.188, T.189, G.190, T.191, S.268, A.297, D.298, Y.303 Ligands: 68W.2 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:K.54, A:A.297 Hydrogen bonds: A:N.84, A:G.185, A:G.187, A:T.188, A:T.189, A:G.190, A:T.191, A:T.191, A:S.268 Water bridges: A:N.160, A:T.188, A:L.192 Salt bridges: A:K.54 PLP.6: 14 residues within 4Å: Chain B: K.54, N.84, G.185, L.186, G.187, T.188, T.189, G.190, T.191, S.268, A.297, D.298, Y.303 Ligands: 68W.7 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:K.54, B:A.297 Hydrogen bonds: B:N.84, B:G.185, B:G.187, B:T.188, B:T.189, B:T.191, B:T.191, B:S.268 Water bridges: B:N.160, B:N.160, B:L.192, B:A.297 Salt bridges: B:K.54

2 x 68W: 3-{[([1,1'-biphenyl]-3-yl)carbamoyl]amino}benzoic acid(Non-covalent)

68W.2: 19 residues within 4Å: Chain A: K.54, G.83, N.84, T.85, G.185, G.187, T.188, A.211, E.212, P.213, A.221, R.223, V.245, A.250, I.267, S.268, A.271 Ligands: PLP.1, ACT.5 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:T.188, A:P.213, A:A.221, A:A.250, A:I.267, A:A.271 Hydrogen bonds: A:N.84, A:T.85, A:T.85, A:T.85, A:R.223 Water bridges: A:R.112, A:A.221, A:L.222 Salt bridges: A:K.54 pi-Cation interactions: A:K.54 68W.7: 22 residues within 4Å: Chain B: K.54, T.81, S.82, G.83, N.84, T.85, Q.154, Y.155, G.185, L.186, G.187, T.188, A.211, E.212, P.213, V.245, A.250, I.267, S.268, A.271, W.325 Ligands: PLP.6 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:T.188, B:A.250, B:I.267, B:A.271, B:W.325 Hydrogen bonds: B:T.81, B:S.82, B:G.83, B:N.84, B:T.85, B:Q.154 Water bridges: B:S.82 Salt bridges: B:K.54

5 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 8 residues within 4Å: Chain A: L.44, D.46, R.47, I.263 Chain B: L.10, N.48, P.49 Ligands: ACT.8 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.263 Hydrogen bonds: A:D.46 Salt bridges: A:R.47 ACT.4: 7 residues within 4Å: Chain A: D.46, N.48, P.49, T.50, G.51 Chain B: D.46, W.301 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.46, B:W.301 ACT.5: 7 residues within 4Å: Chain A: T.81, S.82, G.83, R.112, Y.155, N.224 Ligands: 68W.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.82, A:G.83, A:Y.155 Water bridges: A:N.224 ACT.8: 8 residues within 4Å: Chain A: D.46, W.301 Chain B: D.46, N.48, P.49, T.50, G.51 Ligands: ACT.3 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Water bridges: A:D.46, A:W.301, B:D.46, B:W.301 ACT.9: 6 residues within 4Å: Chain A: L.10, P.49 Chain B: L.44, D.46, R.47, I.263 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.263 Salt bridges: B:R.47

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brunner, K. et al., Inhibitors of the Cysteine Synthase CysM with Antibacterial Potency against Dormant Mycobacterium tuberculosis. J.Med.Chem. (2016)

Release Date

2016-08-17

Peptides

O-phosphoserine sulfhydrylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

O-phosphoserine sulfhydrylase

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