XFEL MT1R structure by ligand exchange from agomelatine to 2-phenylmelatonin.

Experimental Data Snapshot

  • Resolution: 3.30 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.259 
  • R-Value Observed: 0.261 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


Toward G protein-coupled receptor structure-based drug design using X-ray lasers.

Ishchenko, A.Stauch, B.Han, G.W.Batyuk, A.Shiriaeva, A.Li, C.Zatsepin, N.Weierstall, U.Liu, W.Nango, E.Nakane, T.Tanaka, R.Tono, K.Joti, Y.Iwata, S.Moraes, I.Gati, C.Cherezov, V.

(2019) IUCrJ 6: 1106-1119

  • DOI: https://doi.org/10.1107/S2052252519013137
  • Primary Citation of Related Structures:  
    6PRZ, 6PS0, 6PS1, 6PS2, 6PS3, 6PS4, 6PS5, 6PS6, 6PS7, 6PS8

  • PubMed Abstract: 

    Rational structure-based drug design (SBDD) relies on the availability of a large number of co-crystal structures to map the ligand-binding pocket of the target protein and use this information for lead-compound optimization via an iterative process. While SBDD has proven successful for many drug-discovery projects, its application to G protein-coupled receptors (GPCRs) has been limited owing to extreme difficulties with their crystallization. Here, a method is presented for the rapid determination of multiple co-crystal structures for a target GPCR in complex with various ligands, taking advantage of the serial femtosecond crystallography approach, which obviates the need for large crystals and requires only submilligram quantities of purified protein. The method was applied to the human β 2 -adrenergic receptor, resulting in eight room-temperature co-crystal structures with six different ligands, including previously unreported structures with carvedilol and propranolol. The generality of the proposed method was tested with three other receptors. This approach has the potential to enable SBDD for GPCRs and other difficult-to-crystallize membrane proteins.

  • Organizational Affiliation

    Bridge Institute, Departments of Chemistry and Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fusion protein of Melatonin receptor type 1A and GlgA glycogen synthase503Homo sapiensPyrococcus abyssi GE5Mutation(s): 9 
Gene Names: MTNR1APAB2292
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9V2J8 (Pyrococcus abyssi (strain GE5 / Orsay))
Explore Q9V2J8 
Go to UniProtKB:  Q9V2J8
Find proteins for P48039 (Homo sapiens)
Explore P48039 
Go to UniProtKB:  P48039
PHAROS:  P48039
GTEx:  ENSG00000168412 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP48039Q9V2J8
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
JEY (Subject of Investigation/LOI)
Query on JEY

Download Ideal Coordinates CCD File 
B [auth A]N-[2-(5-methoxy-2-phenyl-1H-indol-3-yl)ethyl]acetamide
C19 H20 N2 O2
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on YCM
Binding Affinity Annotations 
IDSourceBinding Affinity
JEY BindingDB:  6PS8 Ki: min: 0.02, max: 0.21 (nM) from 5 assay(s)
IC50: 0.06 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 3.30 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.259 
  • R-Value Observed: 0.261 
  • Space Group: P 4 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.2α = 90
b = 122.2β = 90
c = 122.6γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
CrystFELdata reduction
CrystFELdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35 GM127086

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-13
    Type: Initial release
  • Version 1.1: 2019-12-25
    Changes: Database references
  • Version 1.2: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Refinement description