9C2F

Structure of Calcium-Sensing Receptor in complex with positive allosteric modulator '54149


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Large library docking identifies positive allosteric modulators of the calcium-sensing receptor.

Liu, F.Wu, C.G.Tu, C.L.Glenn, I.Meyerowitz, J.Kaplan, A.L.Lyu, J.Cheng, Z.Tarkhanova, O.O.Moroz, Y.S.Irwin, J.J.Chang, W.Shoichet, B.K.Skiniotis, G.

(2024) Science 385: eado1868-eado1868

  • DOI: https://doi.org/10.1126/science.ado1868
  • Primary Citation of Related Structures:  
    9C1P, 9C2F

  • PubMed Abstract: 

    Positive allosteric modulator (PAM) drugs enhance the activation of the calcium-sensing receptor (CaSR) and suppress parathyroid hormone (PTH) secretion. Unfortunately, these hyperparathyroidism-treating drugs can induce hypocalcemia and arrhythmias. Seeking improved modulators, we docked libraries of 2.7 million and 1.2 billion molecules against the CaSR structure. The billion-molecule docking found PAMs with a 2.7-fold higher hit rate than the million-molecule library, with hits up to 37-fold more potent. Structure-based optimization led to nanomolar leads. In ex vivo organ assays, one of these PAMs was 100-fold more potent than the standard of care, cinacalcet, and reduced serum PTH levels in mice without the hypocalcemia typical of CaSR drugs. As determined from cryo-electron microscopy structures, the PAMs identified here promote CaSR conformations that more closely resemble the activated state than those induced by the established drugs.


  • Organizational Affiliation

    Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94143, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Extracellular calcium-sensing receptor959Homo sapiensMutation(s): 0 
Gene Names: CASRGPRC2APCAR1
UniProt & NIH Common Fund Data Resources
Find proteins for P41180 (Homo sapiens)
Explore P41180 
Go to UniProtKB:  P41180
PHAROS:  P41180
GTEx:  ENSG00000036828 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP41180
Glycosylation
Glycosylation Sites: 3Go to GlyGen: P41180-1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Extracellular calcium-sensing receptor939Homo sapiensMutation(s): 0 
Gene Names: CASRGPRC2APCAR1
UniProt & NIH Common Fund Data Resources
Find proteins for P41180 (Homo sapiens)
Explore P41180 
Go to UniProtKB:  P41180
PHAROS:  P41180
GTEx:  ENSG00000036828 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP41180
Glycosylation
Glycosylation Sites: 3Go to GlyGen: P41180-1
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseC [auth H]2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1ATX (Subject of Investigation/LOI)
Query on A1ATX

Download Ideal Coordinates CCD File 
J [auth A],
V [auth B]
(1R)-1-(2H-1,3-benzodioxol-4-yl)-N-[2-(1,2-benzothiazol-3-yl)ethyl]ethan-1-amine
C18 H18 N2 O2 S
NSLXTKXZHISXFJ-GFCCVEGCSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
D [auth A],
K [auth A],
L [auth A],
N [auth B],
O [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
TRP
Query on TRP

Download Ideal Coordinates CCD File 
H [auth A],
P [auth B]
TRYPTOPHAN
C11 H12 N2 O2
QIVBCDIJIAJPQS-VIFPVBQESA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
I [auth A],
U [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
CA
Query on CA

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
M [auth B]
Q [auth B]
E [auth A],
F [auth A],
G [auth A],
M [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesRO1 NS122394
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesRO1 DK132902

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-02
    Type: Initial release
  • Version 1.1: 2024-11-06
    Changes: Data collection, Structure summary