7F61 | pdb_00007f61

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

PDB DOI: https://doi.org/10.2210/pdb7F61/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens, Escherichia coli
Expression System: Spodoptera frugiperda
Mutation(s): Yes
Membrane Protein: Yes OPM PDBTM MemProtMD mpstruc

Deposited: 2021-06-23 Released: 2022-10-26
Deposition Author(s): Peng, X., Zhang, H.
Funding Organization(s): Ministry of Science and Technology (MoST, China), National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.285 (Depositor), 0.285 (DCC)
R-Value Work:
0.229 (Depositor), 0.229 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

PubMed: 36243875 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-022-33880-y
Primary Citation 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 ₃R 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.

Macromolecule Content

Total Structure Weight: 62.55 kDa
Atom Count: 3,314
Modeled Residue Count: 407
Deposited Residue Count: 554
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histamine H3 receptor	A	407	Homo sapiens	Mutation(s): 1 Gene Names: HRH3, GPCR97 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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9Y5N1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Soluble cytochrome b562	B	147	Escherichia coli	Mutation(s): 3 Gene Names: cybC Membrane Entity: Yes
UniProt
Find proteins for P0ABE7 (Escherichia coli) Explore P0ABE7 Go to UniProtKB: P0ABE7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0ABE7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CLR Query on CLR Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
1IB (Subject of Investigation/LOI) Query on 1IB Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	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		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Binding Affinity Annotations
ID	Source	Binding 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 (Depositor), 0.285 (DCC)
R-Value Work: 0.229 (Depositor), 0.229 (DCC)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.124	α = 90
b = 165.624	β = 90
c = 42.651	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-10-26

Deposition Author(s):

Peng, X.

Zhang, H.

Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2018YFA0508100
National Natural Science Foundation of China (NSFC)	China	81722044
National Natural Science Foundation of China (NSFC)	China	91753115
National Natural Science Foundation of China (NSFC)	China	21778049
National Natural Science Foundation of China (NSFC)	China	81861148018
Ministry of Science and Technology (MoST, China)	China	2018ZX09711002