SMTL ID : 2y1o.1

Dual-target Inhibitor of MurD and MurE Ligases: Design, Synthesis and Binding Mode Studies

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.49 Å

Oligo State

monomer

Ligands

1 x T26: (2R)-2-[[3-[[4-[(Z)-(4-OXO-2-SULFANYLIDENE-1,3-THIAZOLIDIN-5-YLIDENE)METHYL]PHENYL]METHYLAMINO]PHENYL]CARBONYLAMINO]PENTANEDIOIC ACID(Non-covalent)

T26.1: 21 residues within 4Å: Chain A: I.12, G.13, D.36, T.37, R.38, S.72, P.73, G.74, I.140, F.162, H.184, K.320, T.322, A.415, S.416, L.417, N.422, F.423 Ligands: DMS.2, DMS.4, SO4.8 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:F.162, A:A.415 Hydrogen bonds: A:T.37, A:T.37, A:T.322, A:S.416, A:F.423 Water bridges: A:K.116, A:K.116, A:K.116, A:K.116, A:H.184, A:H.184 Salt bridges: A:K.116, A:H.184, A:K.320

4 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.2: 4 residues within 4Å: Chain A: G.74, R.187, L.417 Ligands: T26.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.187 DMS.3: 7 residues within 4Å: Chain A: L.164, T.167, S.168, S.169, L.170, R.201, E.204 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.170 Salt bridges: A:E.204 DMS.4: 7 residues within 4Å: Chain A: P.73, G.138, I.140, S.160, F.162, Q.163 Ligands: T26.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.160 DMS.5: 3 residues within 4Å: Chain A: E.309, H.310, N.311 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.311 Water bridges: A:V.313

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

SO4.6: 7 residues within 4Å: Chain A: N.114, G.115, K.116, S.117, T.118, R.303, K.320 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:G.115, A:G.115, A:S.117, A:T.118 Water bridges: A:N.114, A:K.116, A:K.116, A:K.320, A:S.326 Salt bridges: A:R.303 SO4.7: 4 residues within 4Å: Chain A: H.310, N.311, S.439, H.440 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.311, A:H.440 Salt bridges: A:H.310, A:H.440 SO4.8: 5 residues within 4Å: Chain A: G.15, L.16, T.17, I.140 Ligands: T26.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.16, A:T.17, A:T.17 Water bridges: A:T.17 SO4.9: 2 residues within 4Å: Chain A: R.38, M.39 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.39 Water bridges: A:T.40

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tomasic, T. et al., Dual Inhibitor of MurD and MurE Ligases from Escherichia coli and Staphylococcus aureus. ACS Med Chem Lett (2012)

Release Date

2011-12-28

Peptides

UDP-N-ACETYLMURAMOYLALANINE--D-GLUTAMATE LIGASE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

UDP-N-ACETYLMURAMOYLALANINE--D-GLUTAMATE LIGASE

Related Entries With Identical Sequence