SMTL ID : 2x5o.1

Discovery of Novel 5-Benzylidenerhodanine- and 5-Benzylidene- thiazolidine-2,4-dione Inhibitors of MurD Ligase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.46 Å

Oligo State

monomer

Ligands

1 x VSV: N-({3-[({4-[(Z)-(2,4-DIOXO-1,3-THIAZOLIDIN-5-YLIDENE)METHYL]PHENYL}AMINO)METHYL]PHENYL}CARBONYL)-D-GLUTAMIC ACID(Non-covalent)

VSV.1: 19 residues within 4Å: Chain A: I.11, G.12, D.35, T.36, R.37, S.71, P.72, G.73, I.74, F.161, H.183, R.186, K.348, A.414, S.415, L.416, N.421, F.422 Ligands: SO3.5 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.161, A:A.414, A:L.416 Hydrogen bonds: A:T.36, A:T.36, A:H.183, A:S.415, A:F.422 Salt bridges: A:H.183, A:K.348

1 x AZI: AZIDE ION(Non-covalent)

AZI.2: 5 residues within 4Å: Chain A: L.416, D.417, Q.418, F.419, K.420 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.417, A:F.419

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

SO4.3: 7 residues within 4Å: Chain A: N.113, G.114, K.115, S.116, T.117, R.302, K.319 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.114, A:G.114, A:K.115, A:S.116, A:T.117 Water bridges: A:R.302, A:R.302 Salt bridges: A:R.302 SO4.4: 4 residues within 4Å: Chain A: H.309, N.310, S.438, H.439 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.310, A:H.439 Salt bridges: A:H.309, A:H.439

1 x SO3: SULFITE ION(Non-covalent)

SO3.5: 4 residues within 4Å: Chain A: G.14, L.15, T.16 Ligands: VSV.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.15, A:T.16, A:T.16 Water bridges: A:T.16, A:G.17

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

CL.6: 2 residues within 4Å: Chain A: H.309, N.310 Ligand excluded by PLIP CL.7: 1 residues within 4Å: Chain A: M.38 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain A: E.253, K.254, V.255 Ligand excluded by PLIP CL.9: 1 residues within 4Å: Chain A: N.363 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zidar, N. et al., Discovery of novel 5-benzylidenerhodanine and 5-benzylidenethiazolidine-2,4-dione inhibitors of MurD ligase. J. Med. Chem. (2010)

Release Date

2010-09-15

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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