5Q0S

Ligand binding to FARNESOID-X-RECEPTOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.6 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:  
    5Q0I, 5Q0J, 5Q0K, 5Q0L, 5Q0M, 5Q0N, 5Q0O, 5Q0P, 5Q0Q, 5Q0R, 5Q0S, 5Q0T, 5Q0U, 5Q0V, 5Q0W, 5Q0X, 5Q0Y, 5Q0Z, 5Q10, 5Q11, 5Q12, 5Q13, 5Q14, 5Q15, 5Q16, 5Q17, 5Q18, 5Q19, 5Q1A, 5Q1B, 5Q1C, 5Q1D, 5Q1E, 5Q1F, 5Q1G, 5Q1H, 5Q1I

  • 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. Hoffmann-La Roche ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Bile acid receptorA, C233Homo sapiensMutation(s): 0 
Gene Names: NR1H4BARFXRHRR1RIP14
UniProt & NIH Common Fund Data Resources
Find proteins for Q96RI1 (Homo sapiens)
Explore Q96RI1 
Go to UniProtKB:  Q96RI1
PHAROS:  Q96RI1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96RI1
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
COACTIVATOR PEPTIDE SRC-1 HD3B, D14Homo sapiensMutation(s): 0 
Gene Names: NCOA1BHLHE74SRC1
EC: 2.3.1.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q15788 (Homo sapiens)
Explore Q15788 
Go to UniProtKB:  Q15788
PHAROS:  Q15788
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15788
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9LJ
Query on 9LJ

Download Ideal Coordinates CCD File 
E [auth A],
F [auth C]
(2S)-2-[2-(4-chlorophenyl)-5,6-difluoro-1H-benzimidazol-1-yl]-N-(2-cyanophenyl)-2-cyclohexylacetamide
C28 H23 Cl F2 N4 O
KQOKFDLIIQSPMA-SANMLTNESA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
9LJ BindingDB:  5Q0S IC50: 62 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.169α = 90
b = 84.461β = 90
c = 188.977γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-07-05
    Type: Initial release
  • Version 1.1: 2017-07-19
    Changes: Database references, Structure summary
  • Version 1.2: 2017-12-20
    Changes: Database references
  • Version 1.3: 2018-01-31
    Changes: Database references
  • Version 1.4: 2018-02-21
    Changes: Structure summary
  • Version 1.5: 2021-02-10
    Changes: Database references, Structure summary
  • Version 1.6: 2021-11-17
    Changes: Database references, Structure summary