SMTL ID : 2wjp.1

CRYSTAL STRUCTURE OF MURD LIGASE IN COMPLEX WITH D-GLU CONTAINING RHODANINE INHIBITOR

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

1 x D17: N-({3-[({4-[(Z)-(4-oxo-2-thioxo-1,3-thiazolidin-5-ylidene)methyl]phenyl}amino)methyl]phenyl}carbonyl)-L-glutamic acid(Non-covalent)

D17.1: 20 residues within 4Å: Chain A: I.11, G.12, D.35, T.36, R.37, S.71, P.72, G.73, F.161, H.183, R.186, T.321, K.348, A.414, S.415, L.416, N.421, F.422 Ligands: DMS.2, SO4.11 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.161, A:F.161, A:A.414, A:L.416, A:L.416 Hydrogen bonds: A:T.36, A:T.36, A:S.415, A:F.422 Water bridges: A:T.36, A:T.321 Salt bridges: A:H.183, A:K.348

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

DMS.2: 4 residues within 4Å: Chain A: G.73, R.186, L.416 Ligands: D17.1 No protein-ligand interaction detected (PLIP)

5 x AZI: AZIDE ION(Non-covalent)

AZI.3: 3 residues within 4Å: Chain A: D.417, Q.418, F.419 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.417, A:Q.418 AZI.4: 5 residues within 4Å: Chain A: F.303, A.329, N.331, G.332, L.333 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.332 AZI.5: 6 residues within 4Å: Chain A: L.299, P.300, H.301, R.302, F.422, E.423 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:P.300, A:R.302, A:R.302, A:E.423 AZI.6: 4 residues within 4Å: Chain A: V.335, L.339, N.363, V.364 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.339 AZI.7: 4 residues within 4Å: Chain A: A.102, Q.103, A.104, P.105 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.104 Water bridges: A:I.106

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

SO4.8: 7 residues within 4Å: Chain A: N.113, G.114, K.115, S.116, T.117, R.302, K.319 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:G.114, A:G.114, A:S.116, A:T.117, A:T.117 Water bridges: A:N.113, A:K.115, A:K.115, A:N.271, A:S.325 Salt bridges: A:R.302 SO4.9: 7 residues within 4Å: Chain A: L.163, T.166, S.167, S.168, L.169, R.200, E.203 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.166, A:L.169, A:R.200 SO4.10: 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 SO4.11: 5 residues within 4Å: Chain A: L.13, G.14, L.15, T.16 Ligands: D17.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.15, A:T.16, A:T.16 Water bridges: A:G.17 SO4.12: 2 residues within 4Å: Chain A: R.37, M.38 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.38 Water bridges: A:T.36

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

CL.13: 2 residues within 4Å: Chain A: H.309, N.310 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain A: R.395, L.396 Ligand excluded by PLIP CL.15: 4 residues within 4Å: Chain A: D.2, Y.3, Q.4, R.27 Ligand excluded by PLIP CL.16: 5 residues within 4Å: Chain A: V.92, E.96, T.165, T.166, S.167 Ligand excluded by PLIP CL.17: 3 residues within 4Å: Chain A: S.56, L.57, H.78 Ligand excluded by PLIP CL.18: 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

2010-08-25

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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