2XXI | pdb_00002xxi

Crystal structure of 1-((4-(3-(trifluoromethyl)-6,7-dihydropyrano(4,3- c(pyrazol-1(4H)-yl)phenyl)methyl)-2-pyrrolidinone in complex with the ligand binding domain of the Rat GluA2 receptor and glutamate at 1.6A resolution.

• PDB DOI: https://doi.org/10.2210/pdb2XXI/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2010-11-10 Released: 2011-04-06 
• Deposition Author(s): Ward, S.E., Harries, M., Aldegheri, L., Austin, N.E., Ballantine, S., Ballini, E., Bradley, D.M., Bax, B.D., Clarke, B.P., Harris, A.J., Harrison, S.A., Melarange, R.A., Mookherjee, C., Mosley, J., DalNegro, G., Oliosi, B., Smith, K.J., Thewlis, K.M., Woollard, P.M., Yusaf, S.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.208 (Depositor), 0.219 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Literature

Integration of Lead Optimization with Crystallography for a Membrane-Bound Ion Channel Target: Discovery of a New Class of Ampa Receptor Positive Allosteric Modulators.

Ward, S.E., Harries, M., Aldegheri, L., Austin, N.E., Ballantine, S., Ballini, E., Bradley, D.M., Bax, B.D., Clarke, B.P., Harris, A.J., Harrison, S.A., Melarange, R.A., Mookherjee, C., Mosley, J., Dal Negro, G., Oliosi, B., Smith, K.J., Thewlis, K.M., Woollard, P.M., Yusaf, S.P.

(2011) J Med Chem 54: 78

• PubMed: 21128618 
• DOI: https://doi.org/10.1021/jm100679e
• Primary Citation Related Structures: 
  2XX7, 2XX8, 2XX9, 2XXH, 2XXI


• PubMed Abstract: 
  

  A novel series of AMPAR positive modulators is described that were identified by high throughput screening. The molecules of the series have been optimized from a high quality starting point hit to afford excellent developability, tolerability, and efficacy profiles, leading to identification of a clinical candidate. Unusually for an ion channel target, this optimization was integrated with regular generation of ligand-bound crystal structures and uncovered a novel chemotype with a unique and highly conserved mode of interaction via a trifluoromethyl group.

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Organizational Affiliation: 
• School of Life Sciences, University of Sussex, Brighton, United Kingdom. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 89.18 kDa 
• Atom Count: 6,955 
• Modeled Residue Count: 786 
• Deposited Residue Count: 789 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLUTAMATE RECEPTOR 2	A, B, C	263	Rattus norvegicus	Mutation(s): 1
UniProt
Find proteins for P19491 (Rattus norvegicus) Explore P19491  Go to UniProtKB:  P19491

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
JAC	E [auth A], I [auth B]	1-({4-[3-(TRIFLUOROMETHYL)-6,7-DIHYDROPYRANO[4,3-C]PYRAZOL-1(4H)-YL]PHENYL}METHYL)-2-PYRROLIDINONE C18 H18 F3 N3 O2 URIDIEFPWLZYEF-UHFFFAOYSA-N
GLU	D [auth A], H [auth B], L [auth C]	GLUTAMIC ACID C5 H9 N O4 WHUUTDBJXJRKMK-VKHMYHEASA-N
SO4	F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	G [auth A], J [auth B], K [auth B], M [auth C], N [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.208 (Depositor), 0.219 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.433	α = 90
b = 163.357	β = 90
c = 47.336	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-04-06 
Deposition Author(s): Ward, S.E., Harries, M., Aldegheri, L., Austin, N.E., Ballantine, S., Ballini, E., Bradley, D.M., Bax, B.D., Clarke, B.P., Harris, A.J., Harrison, S.A., Melarange, R.A., Mookherjee, C., Mosley, J., DalNegro, G., Oliosi, B., Smith, K.J., Thewlis, K.M., Woollard, P.M., Yusaf, S.P.

Revision History  

• Version 1.0: 2011-04-06
  Type: Initial release
  
• Version 1.1: 2011-09-28
  Changes: Database references, Version format compliance
• Version 1.2: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Other, Structure summary