5Q17

Ligand binding to FARNESOID-X-RECEPTOR

• PDB DOI:  https://doi.org/10.2210/pdb5Q17/pdb
• Deposition Group: G_1002033 ExploreG_1002033

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-05-31 Released: 2017-07-05 
• Deposition Author(s): Rudolph, M.G., Benz, J., Burger, D., Thoma, R., Ruf, A., Joseph, C., Kuhn, B., Shao, C., Yang, H., Burley, S.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.267 
• R-Value Work: 0.218 
• R-Value Observed: 0.220 

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

• PubMed: 29204945 
• DOI: https://doi.org/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 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 29.13 kDa 
• Atom Count: 2,047 
• Modelled Residue Count: 236 
• Deposited Residue Count: 245 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bile acid receptor	A	233	Homo sapiens	Mutation(s): 0  Gene Names: NR1H4, BAR, FXR, HRR1, RIP14
UniProt & NIH Common Fund Data Resources
Find proteins for Q96RI1 (Homo sapiens) Explore Q96RI1  Go to UniProtKB:  Q96RI1
PHAROS:  Q96RI1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor coactivator peptide SRC2	B	12	Homo sapiens	Mutation(s): 0  Gene Names: NCOA2, BHLHE75, SRC2, TIF2
UniProt & NIH Common Fund Data Resources
Find proteins for Q15596 (Homo sapiens) Explore Q15596  Go to UniProtKB:  Q15596
PHAROS:  Q15596

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
9MV	C [auth A]	4-({5-bromo-2-oxo-1'-[(thiophen-2-yl)sulfonyl]spiro[indole-3,4'-piperidin]-1(2H)-yl}methyl)benzoic acid C24 H21 Br N2 O5 S2 GNPZBVGDUWGWDJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
9MV	BindingDB:  5Q17	IC50: 5640 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.267 
• R-Value Work: 0.218 
• R-Value Observed: 0.220 
• Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.94	α = 90
b = 93.94	β = 90
c = 47.798	γ = 120

Software Package:

Software Name	Purpose
BUSTER	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-07-05 
Deposition Author(s): Rudolph, M.G., Benz, J., Burger, D., Thoma, R., Ruf, A., Joseph, C., Kuhn, B., Shao, C., Yang, H., Burley, S.K.

Revision History  

• 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