Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction | Predict Membrane 

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 53.58 kDa 
• Atom Count: 3555 
• Modelled Residue Count: 428 
• Deposited Residue Count: 452 
• Unique protein chains: 1

3RZE

Structure of the human histamine H1 receptor in complex with doxepin

• PDB DOI: 10.2210/pdb3RZE/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens, Escherichia virus T4
• Expression System: Komagataella pastoris
• Mutation(s): Yes 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2011-05-11 Released: 2011-06-15 
• Deposition Author(s): Shimamura, T., Han, G.W., Shiroishi, M., Weyand, S., Tsujimoto, H., Winter, G., Katritch, V., Abagyan, R., Cherezov, V., Liu, W., Kobayashi, T., Stevens, R., Iwata, S., GPCR Network (GPCR)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.249 
• R-Value Work: 0.214 
• R-Value Observed: 0.217 

Literature

Structure of the human histamine H1 receptor complex with doxepin.

Shimamura, T., Shiroishi, M., Weyand, S., Tsujimoto, H., Winter, G., Katritch, V., Abagyan, R., Cherezov, V., Liu, W., Han, G.W., Kobayashi, T., Stevens, R.C., Iwata, S.

(2011) Nature 475: 65-70

• PubMed: 21697825 
• DOI: 10.1038/nature10236
• Primary Citation of Related Structures:  
  3RZE


• PubMed Abstract: 
  

The biogenic amine histamine is an important pharmacological mediator involved in pathophysiological processes such as allergies and inflammations. Histamine H(1) receptor (H(1)R) antagonists are very effective drugs alleviating the symptoms of allergic reactions. Here we show the crystal structure of the H(1)R complex with doxepin, a first-generation H(1)R antagonist. Doxepin sits deep in the ligand-binding pocket and directly interacts with Trp 428(6.48), a highly conserved key residue in G-protein-coupled-receptor activation. This well-conserved pocket with mostly hydrophobic nature contributes to the low selectivity of the first-generation compounds. The pocket is associated with an anion-binding region occupied by a phosphate ion. Docking of various second-generation H(1)R antagonists reveals that the unique carboxyl group present in this class of compounds interacts with Lys 191(5.39) and/or Lys 179(ECL2), both of which form part of the anion-binding region. This region is not conserved in other aminergic receptors, demonstrating how minor differences in receptors lead to pronounced selectivity differences with small molecules. Our study sheds light on the molecular basis of H(1)R antagonist specificity against H(1)R.

---

Organizational Affiliation: 

Human Receptor Crystallography Project, ERATO, Japan Science and Technology Agency, Kyoto 606-8501, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histamine H1 receptor, Lysozyme chimera	A	452	Homo sapiens, Escherichia virus T4	Mutation(s): 2  Gene Names: HRH1, E EC: 3.2.1.17 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P35367 (Homo sapiens) Explore P35367  Go to UniProtKB:  P35367
PHAROS:  P35367
Find proteins for P00720 (Enterobacteria phage T4) Explore P00720  Go to UniProtKB:  P00720
UniProt Groups	P35367P00720

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OLC	G [auth A]	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C21 H40 O4 RZRNAYUHWVFMIP-GDCKJWNLSA-N
D7V	C [auth A]	(3Z)-3-(dibenzo[b,e]oxepin-11(6H)-ylidene)-N,N-dimethylpropan-1-amine C19 H21 N O ODQWQRRAPPTVAG-BOPFTXTBSA-N
5EH	B [auth A]	(3E)-3-(dibenzo[b,e]oxepin-11(6H)-ylidene)-N,N-dimethylpropan-1-amine C19 H21 N O ODQWQRRAPPTVAG-GZTJUZNOSA-N
PO4	D [auth A], E [auth A], F [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.249 
• R-Value Work: 0.214 
• R-Value Observed: 0.217 
• Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.144	α = 90
b = 88.144	β = 90
c = 331.654	γ = 90

Software Package:

Software Name	Purpose
GDA	data collection
PHASER	phasing
BUSTER	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-05-11 
• Released Date: 2011-06-15 
Deposition Author(s): Shimamura, T., Han, G.W., Shiroishi, M., Weyand, S., Tsujimoto, H., Winter, G., Katritch, V., Abagyan, R., Cherezov, V., Liu, W., Kobayashi, T., Stevens, R., Iwata, S., GPCR Network (GPCR)

Revision History  

• Version 1.0: 2011-06-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-07-20
  Changes: Database references
• Version 1.3: 2017-08-16
  Changes: Refinement description, Source and taxonomy
• Version 1.4: 2018-01-24
  Changes: Structure summary