8GTM

Corticotropin-releasing hormone receptor 1(CRF1R) bound with BMK-C203 by XFEL


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.221 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structure-based drug discovery of a corticotropin-releasing hormone receptor 1 antagonist using an X-ray free-electron laser.

Kim, H.Lim, T.Ha, G.E.Lee, J.Y.Kim, J.W.Chang, N.Kim, S.H.Kim, K.H.Lee, J.Cho, Y.Kim, B.W.Abrahamsson, A.Kim, S.H.Kim, H.J.Park, S.Lee, S.J.Park, J.Cheong, E.Kim, B.M.Cho, H.S.

(2023) Exp Mol Med 55: 2039-2050

  • DOI: https://doi.org/10.1038/s12276-023-01082-1
  • Primary Citation of Related Structures:  
    8GTG, 8GTI, 8GTM

  • PubMed Abstract: 

    Thus far, attempts to develop drugs that target corticotropin-releasing hormone receptor 1 (CRF 1 R), a drug target in stress-related therapy, have been unsuccessful. Studies have focused on using high-resolution G protein-coupled receptor (GPCR) structures to develop drugs. X-ray free-electron lasers (XFELs), which prevent radiation damage and provide access to high-resolution compositions, have helped accelerate GPCR structural studies. We elucidated the crystal structure of CRF 1 R complexed with a BMK-I-152 antagonist at 2.75 Å using fixed-target serial femtosecond crystallography. The results revealed that two unique hydrogen bonds are present in the hydrogen bond network, the stalk region forms an alpha helix and the hydrophobic network contains an antagonist binding site. We then developed two antagonists-BMK-C203 and BMK-C205-and determined the CRF 1 R/BMK-C203 and CRF 1 R/BMK-C205 complex structures at 2.6 and 2.2 Å, respectively. BMK-C205 exerted significant antidepressant effects in mice and, thus, may be utilized to effectively identify structure-based drugs against CRF 1 R.


  • Organizational Affiliation

    Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seoul, 03722, Republic of Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform CRF-R2 of Corticotropin-releasing factor receptor 1284Homo sapiensMutation(s): 11 
Gene Names: CRHR1CRFRCRFR1CRHR
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P34998 (Homo sapiens)
Explore P34998 
Go to UniProtKB:  P34998
PHAROS:  P34998
GTEx:  ENSG00000120088 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP34998
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Endolysin160Enterobacteria phage T6Mutation(s): 2 
Gene Names: eEcT6_00117
EC: 3.2.1.17
UniProt
Find proteins for A0A346FJK3 (Enterobacteria phage T6)
Explore A0A346FJK3 
Go to UniProtKB:  A0A346FJK3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A346FJK3
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
0VI (Subject of Investigation/LOI)
Query on 0VI

Download Ideal Coordinates CCD File 
C [auth A]7-(4-bromanyl-2,6-dimethoxy-phenyl)-4,8-dimethyl-~{N},~{N}-bis[4,4,4-tris(fluoranyl)butyl]-1$l^{4},3,5,9-tetrazabicyclo[4.3.0]nona-1(6),2,4,8-tetraen-2-amine
C23 H27 Br F6 N5 O2
JTEILCBGDKXTJU-SFHVURJKSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.221 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.66α = 90
b = 70.65β = 97.82
c = 86.75γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-09-13
    Type: Initial release
  • Version 1.1: 2023-09-20
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Database references
  • Version 1.3: 2024-11-06
    Changes: Structure summary