ISDA

Entry Detail

PDB ID:

2WJP

Keywords:

LIGASE

Title:

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

Biological Source:

Source Organism:

ESCHERICHIA COLI DH5[ALPHA]

Host Organism:

ESCHERICHIA COLI DH5[ALPHA]

PDB Version:

Deposition Date:

2009-05-28

Release Date:

2010-08-25

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

1.60 Å

R-Value Free:

0.18

R-Value Work:

0.16

R-Value Observed:

0.16

Space Group:

P 41

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Description:UDP-N-ACETYLMURAMOYLALANINE--D-GLUTAMATE LIGASE
Chain IDs:A
Chain Length:439
Number of Molecules:1
Biological Source:ESCHERICHIA COLI DH5[ALPHA]

UniProt ID:P14900 Pfam ID:PF21799, PF08245, PF02875 EC:6.3.2.9

Modified Residue

Compound ID	Chain ID	Parent Comp ID	Details	2D Image
KCX	A	LYS	LYSINE NZ-CARBOXYLIC ACID

Ligand Molecules

AZI

D17

DMS

SO4

Primary Citation

Discovery of Novel 5-Benzylidenerhodanine and 5-Benzylidenethiazolidine-2,4-Dione Inhibitors of Murd Ligase.

Zidar, N, Tomasic, T, Sink, R, Rupnik, V, Kovac, A, Turk, S, Patin, D, Blanot, D, Contreras Martel, C, Dessen, A, Muller Premru, M, Zega, A, Gobec, S, Peterlin Masic, L, Kikelj, D.Show

J.Med.Chem. 53 6584 ? (2010)

PMID: 20804196 DOI: 10.1021/JM100285G

Abstact

We have designed, synthesized, and evaluated 5-benzylidenerhodanine- and 5-benzylidenethiazolidine-2,4-dione-based compounds as inhibitors of bacterial enzyme MurD with E. coli IC(50) in the range 45-206 μM. The high-resolution crystal structure of MurD in complex with (R,Z)-2-(3-[{4-([2,4-dioxothiazolidin-5-ylidene]methyl)phenylamino}methyl)benzamido)pentanedioic acid [(R)-32] revealed details of the binding mode of the inhibitor within the active site and provides a good foundation for structure-based design of a novel generation of MurD inhibitors.

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Protein

Chemical

Disease

Primary Citation of related structures