Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 27.14 kDa 
• Atom Count: 1827 
• Modelled Residue Count: 209 
• Deposited Residue Count: 236 
• Unique protein chains: 1

5FNC

Dynamic Undocking and the Quasi-Bound State as tools for Drug Design

• PDB DOI: 10.2210/pdb5FNC/pdb

• Classification: CHAPERONE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-11-13 Released: 2016-11-23 
• Deposition Author(s): Ruiz-Carmona, S., Schmidtke, P., Luque, F.J., Baker, L.M., Matassova, N., Davis, B., Roughley, S., Murray, J., Hubbard, R., Barril, X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.240 
• R-Value Work: 0.191 
• R-Value Observed: 0.194 

Literature

Dynamic undocking and the quasi-bound state as tools for drug discovery.

Ruiz-Carmona, S., Schmidtke, P., Luque, F.J., Baker, L., Matassova, N., Davis, B., Roughley, S., Murray, J., Hubbard, R., Barril, X.

(2017) Nat Chem 9: 201-206

• PubMed: 28221352 
• DOI: 10.1038/nchem.2660
• Primary Citation of Related Structures:  
  5FNC, 5FND, 5FNF


• PubMed Abstract: 
  

There is a pressing need for new technologies that improve the efficacy and efficiency of drug discovery. Structure-based methods have contributed towards this goal but they focus on predicting the binding affinity of protein-ligand complexes, which is notoriously difficult. We adopt an alternative approach that evaluates structural, rather than thermodynamic, stability. As bioactive molecules present a static binding mode, we devised dynamic undocking (DUck), a fast computational method to calculate the work necessary to reach a quasi-bound state at which the ligand has just broken the most important native contact with the receptor. This non-equilibrium property is surprisingly effective in virtual screening because true ligands form more-resilient interactions than decoys. Notably, DUck is orthogonal to docking and other 'thermodynamic' methods. We demonstrate the potential of the docking-undocking combination in a fragment screening against the molecular chaperone and oncology target Hsp90, for which we obtain novel chemotypes and a hit rate that approaches 40%.

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Organizational Affiliation: 

Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluís Companys 23, 08010 Barcelona, Spain.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HEAT SHOCK PROTEIN, HSP90-ALPHA	A	236	Homo sapiens	Mutation(s): 0  Gene Names: HSP90AA1, HSP90A, HSPC1, HSPCA EC: 3.6.4.10
UniProt & NIH Common Fund Data Resources
Find proteins for P07900 (Homo sapiens) Explore P07900  Go to UniProtKB:  P07900
PHAROS:  P07900

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IEE	B [auth A]	6-CHLORO-4-N-[(4-METHYLPHENYL)METHYL]PYRIMIDINE- 2,4-DIAMINE C12 H13 Cl N4 NOJKOTBYOAEOFZ-UHFFFAOYSA-N
SO4	C [auth A], D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
IEE	Binding MOAD:  5FNC	Kd: 7.70e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.240 
• R-Value Work: 0.191 
• R-Value Observed: 0.194 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.872	α = 90
b = 90.285	β = 90
c = 98.332	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SAINT	data reduction
SADABS	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-11-13 
• Released Date: 2016-11-23 
Deposition Author(s): Ruiz-Carmona, S., Schmidtke, P., Luque, F.J., Baker, L.M., Matassova, N., Davis, B., Roughley, S., Murray, J., Hubbard, R., Barril, X.

Revision History  

• Version 1.0: 2016-11-23
  Type: Initial release
  
• Version 1.1: 2017-03-08
  Changes: Database references
• Version 1.2: 2019-11-06
  Changes: Data collection, Other