7K15 | pdb_00007k15

Crystal structure of the Human Leukotriene B4 Receptor 1 in Complex with Selective Antagonist MK-D-046

• PDB DOI: https://doi.org/10.2210/pdb7K15/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens, Nitratidesulfovibrio vulgaris str. Hildenborough
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2020-09-07 Released: 2021-02-17 
• Deposition Author(s): Michaelian, N., Han, G.W., Cherezov, V.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.88 Å
• R-Value Free: 
  0.261 (Depositor), 0.266 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.216 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Starting Models: experimental

Literature

Structural insights on ligand recognition at the human leukotriene B4 receptor 1.

Michaelian, N., Sadybekov, A., Besserer-Offroy, E., Han, G.W., Krishnamurthy, H., Zamlynny, B.A., Fradera, X., Siliphaivanh, P., Presland, J., Spencer, K.B., Soisson, S.M., Popov, P., Sarret, P., Katritch, V., Cherezov, V.

(2021) Nat Commun 12: 2971-2971

• PubMed: 34016973 
• DOI: https://doi.org/10.1038/s41467-021-23149-1
• Primary Citation Related Structures: 
  7K15


• PubMed Abstract: 
  

  The leukotriene B4 receptor 1 (BLT1) regulates the recruitment and chemotaxis of different cell types and plays a role in the pathophysiology of infectious, allergic, metabolic, and tumorigenic human diseases. Here we present a crystal structure of human BLT1 (hBLT1) in complex with a selective antagonist MK-D-046, developed for the treatment of type 2 diabetes and other inflammatory conditions. Comprehensive analysis of the structure and structure-activity relationship data, reinforced by site-directed mutagenesis and docking studies, reveals molecular determinants of ligand binding and selectivity toward different BLT receptor subtypes and across species. The structure helps to identify a putative membrane-buried ligand access channel as well as potential receptor binding modes of endogenous agonists. These structural insights of hBLT1 enrich our understanding of its ligand recognition and open up future avenues in structure-based drug design.

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Organizational Affiliation: 
• Bridge Institute, USC Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA, USA.
Department of Chemistry, University of Southern California, Los Angeles, CA, USA.
Department of Pharmacology-Physiology, Faculty of Medicine and Health Sciences, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke, QC, Canada.
Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, USA.
Merck Research Laboratories, Merck & Co., Inc., Kenilworth, NJ, USA.
Center for Computational and Data Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Moscow, Russia.
Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.
Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA.
Bridge Institute, USC Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA, USA. [e-mail].
Department of Chemistry, University of Southern California, Los Angeles, CA, USA. [e-mail].
Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 56.14 kDa 
• Atom Count: 3,624 
• Modeled Residue Count: 455 
• Deposited Residue Count: 490 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Leukotriene B4 receptor 1,Flavodoxin,Leukotriene B4 receptor 1	A	490	Homo sapiens, Nitratidesulfovibrio vulgaris str. Hildenborough	Mutation(s): 7  Gene Names: LTB4R, BLT, BLT1, BLTR, CMKRL1, GPR16, P2RY7, DVU_2680 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P00323 (Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough)) Explore P00323  Go to UniProtKB:  P00323
Find proteins for Q15722 (Homo sapiens) Explore Q15722  Go to UniProtKB:  Q15722
PHAROS:  Q15722 GTEx:  ENSG00000213903
UniProt Groups	Q15722P00323

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
VRJ (Subject of Investigation/LOI)	B [auth A]	N-(tert-butylsulfonyl)-4-fluoro-2-{(3S,4R)-4-hydroxy-3-[(pyridin-2-yl)methyl]-3,4-dihydro-2H-1-benzopyran-7-yl}benzamide C26 H27 F N2 O5 S DJXXSNJFTPBZSH-BXKMTCNYSA-N
FMN	D [auth A]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
2PE	I [auth A]	NONAETHYLENE GLYCOL C18 H38 O10 YZUUTMGDONTGTN-UHFFFAOYSA-N
OLC	F [auth A], G [auth A]	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C21 H40 O4 RZRNAYUHWVFMIP-GDCKJWNLSA-N
OLA	E [auth A]	OLEIC ACID C18 H34 O2 ZQPPMHVWECSIRJ-KTKRTIGZSA-N
P6G	J [auth A]	HEXAETHYLENE GLYCOL C12 H26 O7 IIRDTKBZINWQAW-UHFFFAOYSA-N
1PE	H [auth A]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.88 Å
• R-Value Free:  0.261 (Depositor), 0.266 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.216 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: P 2₁ 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.77	α = 90
b = 82.67	β = 90
c = 127.48	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-02-17 
Deposition Author(s): Michaelian, N., Han, G.W., Cherezov, V.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35 GM127086

Revision History  

• Version 1.0: 2021-02-17
  Type: Initial release
  
• Version 1.1: 2021-06-02
  Changes: Database references
• Version 1.2: 2023-10-18
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-10-16
  Changes: Structure summary