5A8E

thermostabilised beta1-adrenoceptor with rationally designed inverse agonist 7-methylcyanopindolol bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Pharmacological Analysis and Structure Determination of 7-Methylcyanopindolol-Bound Beta1-Adrenergic Receptor.

Sato, T.Baker, J.Warne, T.Brown, G.Leslie, A.Congreve, M.Tate, C.

(2015) Mol.Pharmacol. 88: 1024

  • DOI: 10.1124/mol.115.101030

  • PubMed Abstract: 
  • Comparisons between structures of the β1-adrenergic receptor (AR) bound to either agonists, partial agonists, or weak partial agonists led to the proposal that rotamer changes of Ser(5.46), coupled to a contraction of the binding pocket, are sufficie ...

    Comparisons between structures of the β1-adrenergic receptor (AR) bound to either agonists, partial agonists, or weak partial agonists led to the proposal that rotamer changes of Ser(5.46), coupled to a contraction of the binding pocket, are sufficient to increase the probability of receptor activation. (RS)-4-[3-(tert-butylamino)-2-hydroxypropoxy]-1H-indole-2-carbonitrile (cyanopindolol) is a weak partial agonist of β1AR and, based on the hypothesis above, we predicted that the addition of a methyl group to form 4-[(2S)-3-(tert-butylamino)-2-hydroxypropoxy]-7-methyl-1H-indole-2-carbonitrile (7-methylcyanopindolol) would dramatically reduce its efficacy. An eight-step synthesis of 7-methylcyanopindolol was developed and its pharmacology was analyzed. 7-Methylcyanopindolol bound with similar affinity to cyanopindolol to both β1AR and β2AR. As predicted, the efficacy of 7-methylcyanopindolol was reduced significantly compared with cyanopindolol, acting as a very weak partial agonist of turkey β1AR and an inverse agonist of human β2AR. The structure of 7-methylcyanopindolol-bound β1AR was determined to 2.4-Å resolution and found to be virtually identical to the structure of cyanopindolol-bound β1AR. The major differences in the orthosteric binding pocket are that it has expanded by 0.3 Å in 7-methylcyanopindolol-bound β1AR and the hydroxyl group of Ser(5.46) is positioned 0.8 Å further from the ligand, with respect to the position of the Ser(5.46) side chain in cyanopindolol-bound β1AR. Thus, the molecular basis for the reduction in efficacy of 7-methylcyanopindolol compared with cyanopindolol may be regarded as the opposite of the mechanism proposed for the increase in efficacy of agonists compared with antagonists.


    Organizational Affiliation

    MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom (T.S., T.W., A.G.W.L., C.G.T.); Heptares Therapeutics Ltd, Welwyn Garden City, United Kingdom (G.A.B., M.C.); School of Life Sciences, University of Nottingham, Medical School, Queen's Medical Centre, Nottingham, United Kingdom (J.B.); KEK High Energy Accelerator Research Organization, Institute of Materials Structure Science, Structural Biology Research Center, Tsukuba, Japan (T.S.).




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BETA1 ADRENERGIC RECEPTOR
A
315Meleagris gallopavoMutation(s): 11 
Gene Names: ADRB1
Find proteins for P07700 (Meleagris gallopavo)
Go to Gene View: ADRB1
Go to UniProtKB:  P07700
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OLC
Query on OLC

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A
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
1-Oleoyl-R-glycerol
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
 Ligand Interaction
NA
Query on NA

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A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
MHA
Query on MHA

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Download CCD File 
A
(CARBAMOYLMETHYL-CARBOXYMETHYL-AMINO)-ACETIC ACID
N-(2-ACETAMIDO)IMINODIACETIC ACID
C6 H10 N2 O5
QZTKDVCDBIDYMD-UHFFFAOYSA-N
 Ligand Interaction
XTK
Query on XTK

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Download CCD File 
A
4-[(2S)-3-(tert-butylamino)-2-hydroxypropoxy]-7-methyl-1H-indole-2-carbonitrile
C17 H23 N3 O2
NDCOGBYMSDLXAU-ZDUSSCGKSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.217 
  • Space Group: P 21 2 21
Unit Cell:
Length (Å)Angle (°)
a = 53.019α = 90.00
b = 61.777β = 90.00
c = 95.561γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
Aimlessdata scaling
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-09-30
    Type: Initial release
  • Version 1.1: 2015-11-11
    Type: Database references