7F61

Crystal structure of human histamine receptor H3R in complex with antagonist PF03654746


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.229 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structural basis for recognition of antihistamine drug by human histamine receptor.

Peng, X.Yang, L.Liu, Z.Lou, S.Mei, S.Li, M.Chen, Z.Zhang, H.

(2022) Nat Commun 13: 6105-6105

  • DOI: https://doi.org/10.1038/s41467-022-33880-y
  • Primary Citation of Related Structures:  
    7F61

  • PubMed Abstract: 

    The histamine receptors belong to the G protein-coupled receptor (GPCR) superfamily, and play important roles in the regulation of histamine and other neurotransmitters in the central nervous system, as potential targets for the treatment of neurologic and psychiatric disorders. Here we report the crystal structure of human histamine receptor H 3 R bound to an antagonist PF-03654746 at 2.6 Å resolution. Combined with the computational and functional assays, our structure reveals binding modes of the antagonist and allosteric cholesterol. Molecular dynamic simulations and molecular docking of different antihistamines further elucidate the conserved ligand-binding modes. These findings are therefore expected to facilitate the structure-based design of novel antihistamines.


  • Organizational Affiliation

    Hangzhou Institute of Innovative Medicine, Institute of Pharmacology and Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, 310058, Hangzhou, Zhejiang, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histamine H3 receptor407Homo sapiensMutation(s): 1 
Gene Names: HRH3GPCR97
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y5N1 (Homo sapiens)
Explore Q9Y5N1 
Go to UniProtKB:  Q9Y5N1
PHAROS:  Q9Y5N1
GTEx:  ENSG00000101180 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y5N1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Soluble cytochrome b562147Escherichia coliMutation(s): 3 
Gene Names: cybC
Membrane Entity: Yes 
UniProt
Find proteins for P0ABE7 (Escherichia coli)
Explore P0ABE7 
Go to UniProtKB:  P0ABE7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ABE7
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLR
Query on CLR

Download Ideal Coordinates CCD File 
D [auth A]CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
1IB (Subject of Investigation/LOI)
Query on 1IB

Download Ideal Coordinates CCD File 
C [auth A]N-ethyl-3-fluoranyl-3-[3-fluoranyl-4-(pyrrolidin-1-ylmethyl)phenyl]cyclobutane-1-carboxamide
C18 H24 F2 N2 O
SXMBKHYDZOCBMT-PPUGGXLSSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
1IB BindingDB:  7F61 Ki: min: 1.7, max: 37.15 (nM) from 7 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.229 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.124α = 90
b = 165.624β = 90
c = 42.651γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China2018YFA0508100
National Natural Science Foundation of China (NSFC)China81722044
National Natural Science Foundation of China (NSFC)China91753115
National Natural Science Foundation of China (NSFC)China21778049
National Natural Science Foundation of China (NSFC)China81861148018
Ministry of Science and Technology (MoST, China)China2018ZX09711002

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-26
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-10-23
    Changes: Structure summary