5X2L

Crystal Structure of Human Serine Racemase

• PDB DOI: https://doi.org/10.2210/pdb5X2L/pdb

• Classification: LYASE, ISOMERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-02-01 Released: 2018-01-31 
• Deposition Author(s): Obita, T., Matsumoto, K., Mori, H., Toyooka, N., Mizuguchi, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free: 0.258 
• R-Value Work: 0.220 
• R-Value Observed: 0.222 

Literature

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.

(2017) Bioorg Med Chem Lett 

• PubMed: 29277459 
• DOI: https://doi.org/10.1016/j.bmcl.2017.12.021
• Primary Citation of Related Structures:  
  5X2L


• PubMed Abstract: 
  

  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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Organizational Affiliation: 

Graduate School of Innovative Life Science, University of Toyama, Japan.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 75.89 kDa 
• Atom Count: 4,966 
• Modelled Residue Count: 612 
• Deposited Residue Count: 696 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine racemase	A, B	348	Homo sapiens	Mutation(s): 0  Gene Names: SRR EC: 5.1.1.18 (PDB Primary Data), 4.3.1.18 (PDB Primary Data), 4.3.1.17 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9GZT4 (Homo sapiens) Explore Q9GZT4  Go to UniProtKB:  Q9GZT4
PHAROS:  Q9GZT4 GTEx:  ENSG00000167720

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	C [auth A], E [auth B]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
MG	D [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free: 0.258 
• R-Value Work: 0.220 
• R-Value Observed: 0.222 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.12	α = 90
b = 112.59	β = 90
c = 88	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-01-31 
Deposition Author(s): Obita, T., Matsumoto, K., Mori, H., Toyooka, N., Mizuguchi, M.

Revision History  

• Version 1.0: 2018-01-31
  Type: Initial release
  
• Version 1.1: 2021-02-24
  Changes: Derived calculations