5Q1E

Ligand binding to FARNESOID-X-RECEPTOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

D3R Grand Challenge 2: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies.

Gaieb, Z.Liu, S.Gathiaka, S.Chiu, M.Yang, H.Shao, C.Feher, V.A.Walters, W.P.Kuhn, B.Rudolph, M.G.Burley, S.K.Gilson, M.K.Amaro, R.E.

(2018) J. Comput. Aided Mol. Des. 32: 1-20

  • DOI: 10.1007/s10822-017-0088-4
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The Drug Design Data Resource (D3R) ran Grand Challenge 2 (GC2) from September 2016 through February 2017. This challenge was based on a dataset of structures and affinities for the nuclear receptor farnesoid X receptor (FXR), contributed by F. Hoffm ...

    The Drug Design Data Resource (D3R) ran Grand Challenge 2 (GC2) from September 2016 through February 2017. This challenge was based on a dataset of structures and affinities for the nuclear receptor farnesoid X receptor (FXR), contributed by F. Hoffmann-La Roche. The dataset contained 102 IC50 values, spanning six orders of magnitude, and 36 high-resolution co-crystal structures with representatives of four major ligand classes. Strong global participation was evident, with 49 participants submitting 262 prediction submission packages in total. Procedurally, GC2 mimicked Grand Challenge 2015 (GC2015), with a Stage 1 subchallenge testing ligand pose prediction methods and ranking and scoring methods, and a Stage 2 subchallenge testing only ligand ranking and scoring methods after the release of all blinded co-crystal structures. Two smaller curated sets of 18 and 15 ligands were developed to test alchemical free energy methods. This overview summarizes all aspects of GC2, including the dataset details, challenge procedures, and participant results. We also consider implications for progress in the field, while highlighting methodological areas that merit continued development. Similar to GC2015, the outcome of GC2 underscores the pressing need for methods development in pose prediction, particularly for ligand scaffolds not currently represented in the Protein Data Bank ( http://www.pdb.org ), and in affinity ranking and scoring of bound ligands.


    Organizational Affiliation

    Drug Design Data Resource, University of California, San Diego, La Jolla, CA, 92093, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Bile acid receptor
A
233Homo sapiensMutation(s): 0 
Gene Names: NR1H4 (BAR, FXR, HRR1, RIP14)
Find proteins for Q96RI1 (Homo sapiens)
Go to Gene View: NR1H4
Go to UniProtKB:  Q96RI1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
COACTIVATOR PEPTIDE SRC-1 HD3
B
14Homo sapiensMutation(s): 0 
Gene Names: NCOA1 (BHLHE74, SRC1)
EC: 2.3.1.48
Find proteins for Q15788 (Homo sapiens)
Go to Gene View: NCOA1
Go to UniProtKB:  Q15788
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9NG
Query on 9NG

Download SDF File 
Download CCD File 
A
N-{2-[(3R)-5-bromo-2-oxo-1-{[4-(1H-tetrazol-5-yl)phenyl]methyl}-2,3-dihydro-1H-indol-3-yl]ethyl}-N-ethylthiophene-2-sulfonamide
C24 H23 Br N6 O3 S2
FAHSKKCLSLGRSF-LJQANCHMSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.188 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 93.305α = 90.00
b = 93.305β = 90.00
c = 47.898γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data scaling
HKL-2000data reduction
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-07-05
    Type: Initial release
  • Version 1.1: 2017-07-19
    Type: Database references, Structure summary
  • Version 1.2: 2017-12-20
    Type: Database references
  • Version 1.3: 2018-01-31
    Type: Database references
  • Version 1.4: 2018-02-21
    Type: Structure summary