ISDA

Deposition Date 2017-02-01

Release Date 2018-01-31

Last Version Date 2025-04-09

Entry Detail

PDB ID:

5X2L

Keywords:

LYASE, ISOMERASE

Title:

Crystal Structure of Human Serine Racemase

Biological Source:

Source Organism:

Homo sapiens (Taxon ID: 9606)

Host Organism:

Escherichia coli

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

1.81 Å

R-Value Free:

0.25

R-Value Work:

0.22

R-Value Observed:

0.22

Space Group:

P 21 21 2

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Serine racemase
Gene (Uniprot):SRR
Chain IDs:A, B
Chain Length:348
Number of Molecules:2
Biological Source:Homo sapiens

UniProt ID:Q9GZT4 Pfam ID:PF00291 EC:5.1.1.18

Ligand Molecules

PLP

Primary Citation

Design, synthesis, and evaluation of novel inhibitors for wild-type human serine racemase.

Takahara, S, Nakagawa, K, Uchiyama, T, Yoshida, T, Matsumoto, K, Kawasumi, Y, Mizuguchi, M, Obita, T, Watanabe, Y, Hayakawa, D, Gouda, H, Mori, H, Toyooka, N.Show

Bioorg. Med. Chem. Lett. ? ? ? (2017)

PMID: 29277459 DOI: 10.1016/j.bmcl.2017.12.021

Abstact

Most of the endogenous free d-serine (about 90%) in the brain is produced by serine racemase (SR). d-Serine in the brain is involved in neurodegenerative disorders and epileptic states as an endogenous co-agonist of the NMDA-type glutamate receptor. Thus, SR inhibitors are expected to be novel therapeutic candidates for the treatment of these disorders. In this study, we solved the crystal structure of wild-type SR, and tried to identify a new inhibitor of SR by in silico screening using the structural information. As a result, we identified two hit compounds by their in vitro evaluations using wild-type SR. Based on the structure of the more potent hit compound 1, we synthesized 15 derivatives and evaluated their inhibitory activities against wild-type SR. Among them, the compound 9C showed relatively high inhibitory potency for wild-type SR. Compound 9C was a more potent inhibitor than compound 24, which was synthesized by our group based upon the structural information of the mutant-type SR.

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Primary Citation of related structures