2XHD | pdb_00002xhd

Crystal structure of N-((2S)-5-(6-fluoro-3-pyridinyl)-2,3-dihydro-1H- inden-2-yl)-2-propanesulfonamide in complex with the ligand binding domain of the human GluA2 receptor

• PDB DOI: https://doi.org/10.2210/pdb2XHD/pdb

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


• Deposited: 2010-06-14 Released: 2010-07-21 
• Deposition Author(s): Ward, S.E., Harries, M., Aldegheri, L., Andreotti, D., Ballantine, S., Bax, B.D., Harris, A.J., Harker, A.J., Lund, J., Melarange, R., Mingardi, A., Mookherjee, C., Mosley, J., Neve, M., Oliosi, B., Profeta, R., Smith, K.J., Smith, P.W., Spada, S., Thewlis, K.M., Yusaf, S.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.238 (Depositor), 0.237 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Literature

Discovery of N-[(2S)-5-(6-Fluoro-3-Pyridinyl)-2,3-Dihydro-1H-Inden-2-Yl]-2-Propanesulfonamide, a Novel Clinical Ampa Receptor Positive Modulator.

Ward, S.E., Harries, M., Aldegheri, L., Andreotti, D., Ballantine, S., Bax, B.D., Harris, A.J., Harker, A.J., Lund, J., Melarange, R., Mingardi, A., Mookherjee, C., Mosley, J., Neve, M., Oliosi, B., Profeta, R., Smith, K.J., Smith, P.W., Spada, S., Thewlis, K.M., Yusaf, S.P.

(2010) J Med Chem 53: 5801

• PubMed: 20614889 
• DOI: https://doi.org/10.1021/jm1005429
• Primary Citation Related Structures: 
  2XHD


• PubMed Abstract: 
  

  A series of AMPA receptor positive allosteric modulators has been optimized from poorly penetrant leads to identify molecules with excellent preclinical pharmacokinetics and CNS penetration. These discoveries led to 17i, a potent, efficacious CNS penetrant molecule with an excellent pharmacokinetic profile across preclinical species, which is well tolerated and is also orally bioavailable in humans.

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Organizational Affiliation: 
• Neurosciences Centre of Excellence for Drug Discovery, GlaxoSmithKline, New Frontiers Science Park, Harlow, Essex, UK. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 59.66 kDa 
• Atom Count: 4,834 
• Modeled Residue Count: 517 
• Deposited Residue Count: 526 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLUTAMATE RECEPTOR 2	A, B	263	Homo sapiens	Mutation(s): 1
UniProt & NIH Common Fund Data Resources
Find proteins for P42262 (Homo sapiens) Explore P42262  Go to UniProtKB:  P42262
PHAROS:  P42262 GTEx:  ENSG00000120251

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
7T9	G [auth B]	N-[(2S)-5-(6-FLUORO-3-PYRIDINYL)-2,3-DIHYDRO-1H-INDEN-2-YL]-2-PROPANESULFONAMIDE C17 H19 F N2 O2 S QXQSUBKWSHMXDP-INIZCTEOSA-N
GLU	C [auth A], F [auth B]	GLUTAMIC ACID C5 H9 N O4 WHUUTDBJXJRKMK-VKHMYHEASA-N
SO4	D [auth A], E [auth A], H [auth B], I [auth B], J [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.238 (Depositor), 0.237 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.139	α = 90
b = 121.781	β = 90
c = 47.49	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-07-21 
Deposition Author(s): Ward, S.E., Harries, M., Aldegheri, L., Andreotti, D., Ballantine, S., Bax, B.D., Harris, A.J., Harker, A.J., Lund, J., Melarange, R., Mingardi, A., Mookherjee, C., Mosley, J., Neve, M., Oliosi, B., Profeta, R., Smith, K.J., Smith, P.W., Spada, S., Thewlis, K.M., Yusaf, S.P.

Revision History  

• Version 1.0: 2010-07-21
  Type: Initial release
  
• Version 1.1: 2011-05-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Other, Structure summary