SMTL ID : 2y68.1

Structure-based design of a new series of D-glutamic acid-based inhibitors of bacterial MurD ligase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.49 Å

Oligo State

monomer

Ligands

1 x T04: 2-[[2-fluoro-5-[[[4-[(Z)-(4-oxo-2-sulfanylidene-1,3-thiazolidin-5-ylidene)methyl]phenyl]amino]methyl]phenyl]carbonylamino]pentanedioic acid(Non-covalent)

T04.1: 20 residues within 4Å: Chain A: I.12, G.13, D.36, T.37, R.38, S.72, G.74, I.75, N.139, S.160, F.162, H.184, T.322, K.349, A.415, S.416, L.417, N.422, F.423 Ligands: SO4.10 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.162, A:A.415, A:L.417 Hydrogen bonds: A:T.37, A:T.37, A:S.416, A:F.423 Water bridges: A:T.322 Salt bridges: A:H.184, A:K.349

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

DMS.2: 7 residues within 4Å: Chain A: L.164, T.167, S.168, S.169, L.170, R.201, E.204 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.170 DMS.3: 3 residues within 4Å: Chain A: E.309, H.310, N.311 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.311

4 x AZI: AZIDE ION(Non-covalent)

AZI.4: 5 residues within 4Å: Chain A: L.417, D.418, Q.419, F.420, K.421 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.418, A:F.420 AZI.5: 6 residues within 4Å: Chain A: F.304, A.329, A.330, N.332, G.333, L.334 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.329 AZI.6: 4 residues within 4Å: Chain A: V.336, L.340, N.364, V.365 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.340, A:N.364 AZI.7: 4 residues within 4Å: Chain A: A.103, Q.104, A.105, P.106 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.104 Water bridges: A:A.103, A:I.107

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

SO4.8: 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, A:T.118 Water bridges: A:N.114, A:K.116, A:K.116, A:S.326 Salt bridges: A:R.303 SO4.9: 4 residues within 4Å: Chain A: H.310, N.311, S.439, H.440 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.311, A:H.440 Water bridges: A:N.311 Salt bridges: A:H.310, A:H.440 SO4.10: 5 residues within 4Å: Chain A: L.14, G.15, L.16, T.17 Ligands: T04.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.16, A:T.17, A:T.17, A:G.18 SO4.11: 2 residues within 4Å: Chain A: R.38, M.39 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.39

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.12: 2 residues within 4Å: Chain A: R.396, L.397 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain A: S.57, L.58 Ligand excluded by PLIP CL.14: 1 residues within 4Å: Chain A: N.364 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tomasic, T. et al., Structure-based design of a new series of D-glutamic acid based inhibitors of bacterial UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase (MurD). J. Med. Chem. (2011)

Release Date

2011-06-08

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

UDP-N-ACETYLMURAMOYLALANINE--D-GLUTAMATE LIGASE

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