3ZPQ

Thermostabilised turkey beta1 adrenergic receptor with 4-(piperazin-1- yl)-1H-indole bound (compound 19)

• PDB DOI: https://doi.org/10.2210/pdb3ZPQ/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Meleagris gallopavo
• Expression System: Trichoplusia ni
• Mutation(s): Yes 
• Membrane Protein: Yes  PDBTMMemProtMD


• Deposited: 2013-03-01 Released: 2013-04-03 
• Deposition Author(s): Christopher, J.A., Congreve, M., Dore, A.S., Marshall, F.H., Myszka, D.G., Brown, J., Koglin, M., Tehan, B., Errey, J.C., Tate, C.G., Warne, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.274 
• R-Value Work: 0.220 
• R-Value Observed: 0.223 

Starting Model: experimental

Literature

Biophysical Fragment Screening of the Beta1-Adrenergic Receptor: Identification of High Affinity Aryl Piperazine Leads Using Structure-Based Drug Design.

Christopher, J., Brown, J., Dore, A., Errey, J., Koglin, M., Marshall, F.H., Myszka, D., Rich, R.L., Tate, C.G., Tehan, B., Warne, T., Congreve, M.

(2013) J Med Chem 56: 3446

• PubMed: 23517028 
• DOI: https://doi.org/10.1021/jm400140q
• Primary Citation of Related Structures:  
  3ZPQ, 3ZPR


• PubMed Abstract: 
  

  Biophysical fragment screening of a thermostabilized β1-adrenergic receptor (β1AR) using surface plasmon resonance (SPR) enabled the identification of moderate affinity, high ligand efficiency (LE) arylpiperazine hits 7 and 8. Subsequent hit to lead follow-up confirmed the activity of the chemotype, and a structure-based design approach using protein-ligand crystal structures of the β1AR resulted in the identification of several fragments that bound with higher affinity, including indole 19 and quinoline 20. In the first example of GPCR crystallography with ligands derived from fragment screening, structures of the stabilized β1AR complexed with 19 and 20 were determined at resolutions of 2.8 and 2.7 Å, respectively.

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Organizational Affiliation: 

Heptares Therapeutics Ltd. , BioPark, Welwyn Garden City, Hertfordshire, AL7 3AX, U.K. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 77.72 kDa 
• Atom Count: 4,996 
• Modelled Residue Count: 586 
• Deposited Residue Count: 630 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BETA-1 ADRENERGIC RECEPTOR	A, B	315	Meleagris gallopavo	Mutation(s): 8  Membrane Entity: Yes
UniProt
Find proteins for P07700 (Meleagris gallopavo) Explore P07700  Go to UniProtKB:  P07700

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
Y01	C [auth A], D [auth A], K [auth B], L [auth B]	CHOLESTEROL HEMISUCCINATE C31 H50 O4 WLNARFZDISHUGS-MIXBDBMTSA-N
2CV	E [auth A], F [auth A], G [auth A], H [auth A], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B]	HEGA-10 C18 H37 N O7 ITEIKACYSCODFV-ATLSCFEFSA-N
XF5	I [auth A], S [auth B]	4-(PIPERAZIN-1-YL)-1H-INDOLE C12 H15 N3 YZKSXUIOKWQABW-UHFFFAOYSA-N
NA	J [auth A], R [auth B], T [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
XF5	PDBBind:  3ZPQ	Ki: 67.6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.274 
• R-Value Work: 0.220 
• R-Value Observed: 0.223 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.852	α = 90
b = 61.441	β = 108.89
c = 100.784	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-04-03 
Deposition Author(s): Christopher, J.A., Congreve, M., Dore, A.S., Marshall, F.H., Myszka, D.G., Brown, J., Koglin, M., Tehan, B., Errey, J.C., Tate, C.G., Warne, T.

Revision History  

• Version 1.0: 2013-04-03
  Type: Initial release
  
• Version 1.1: 2013-05-22
  Changes: Database references
• Version 1.2: 2019-04-03
  Changes: Data collection, Other, Source and taxonomy
• Version 1.3: 2019-05-15
  Changes: Data collection, Experimental preparation
• Version 1.4: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.5: 2024-11-13
  Changes: Structure summary