SMTL ID : 5i6d.1 (1 other biounit)

Mycobacterium tuberculosis CysM in complex with the Urea-scaffold inhibitor 5 [3-(3-(p-Tolyl)ureido) benzoic acid]

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.64 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 Ligands: AU6.2, GOL.3 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:T.188, A:T.188, A:L.192 Salt bridges: A:K.54 PLP.4: 13 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 Ligands: AU6.5 16 PLIP interactions: 16 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:G.190, B:T.191, B:T.191, B:S.268 Water bridges: B:R.112, B:N.160, B:N.160, B:L.192 Salt bridges: B:K.54

2 x AU6: 3-{[(4-methylphenyl)carbamoyl]amino}benzoic acid(Non-covalent)

AU6.2: 19 residues within 4Å: Chain A: 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, S.268, A.271 Ligands: PLP.1, GOL.3 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:T.188, A:P.213, A:A.271 Hydrogen bonds: A:S.82, A:G.83, A:N.84, A:T.85, A:Q.154 Water bridges: A:S.82, A:S.82 Salt bridges: A:K.54 AU6.5: 18 residues within 4Å: Chain B: K.54, T.81, S.82, G.83, N.84, T.85, Q.154, Y.155, G.185, G.187, T.188, A.211, E.212, P.213, S.268, A.271 Ligands: PLP.4, GOL.6 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:T.188, B:P.213, B:A.271 Hydrogen bonds: B:T.81, B:S.82, B:G.83, B:N.84, B:T.85, B:T.85, B:Q.154 Salt bridges: B:K.54 pi-Cation interactions: B:K.54

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: N.84, R.112, Y.303 Ligands: PLP.1, AU6.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.84, A:R.112 Water bridges: A:S.82, A:S.82, A:S.82 GOL.6: 3 residues within 4Å: Chain B: S.82, S.132 Ligands: AU6.5 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.82, B:S.132 Water bridges: B:R.112, B:S.132

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
A

B
B

O-phosphoserine sulfhydrylase

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