5A2S | pdb_00005a2s

Potent, selective and CNS-penetrant tetrasubstituted cyclopropane class IIa histone deacetylase (HDAC) inhibitors

• PDB DOI: https://doi.org/10.2210/pdb5A2S/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2015-05-22 Released: 2016-02-10 
• Deposition Author(s): Luckhurst, C.A., Breccia, P., Stott, A.J., Aziz, O., Birch, H., Burli, R.W., Hughes, S., Jarvis, R.E., Lamers, M., Leonard, P., Matthews, K.L., McAllister, G., Pollack, S., Saville-Stones, E., Wishart, G., Yates, D., Dominguez, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 
  0.256 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Model: experimental

Literature

Potent, Selective, and Cns-Penetrant Tetrasubstituted Cyclopropane Class Iia Histone Deacetylase (Hdac) Inhibitors.

Luckhurst, C.A., Breccia, P., Stott, A.J., Aziz, O., Birch, H.L., Burli, R.W., Hughes, S.J., Jarvis, R.E., Lamers, M., Leonard, P.M., Matthews, K.L., Mcallister, G., Pollack, S., Saville-Stones, E., Wishart, G., Yates, D., Dominguez, C.

(2016) ACS Med Chem Lett 7: 34

• PubMed: 26819662 
• DOI: https://doi.org/10.1021/acsmedchemlett.5b00302
• Primary Citation of Related Structures:  
  5A2S


• PubMed Abstract: 
  

  Potent and selective class IIa HDAC tetrasubstituted cyclopropane hydroxamic acid inhibitors were identified with high oral bioavailability that exhibited good brain and muscle exposure. Compound 14 displayed suitable properties for assessment of the impact of class IIa HDAC catalytic site inhibition in preclinical disease models.

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Organizational Affiliation: 

BioFocus, Charles River , Chesterford Research Park, Saffron Walden, Essex, CB10 1XL, United Kingdom.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 86.55 kDa 
• Atom Count: 5,783 
• Modelled Residue Count: 760 
• Deposited Residue Count: 790 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HISTONE DEACETYLASE 4	A, B	395	Homo sapiens	Mutation(s): 1  EC: 3.5.1.98
UniProt & NIH Common Fund Data Resources
Find proteins for P56524 (Homo sapiens) Explore P56524  Go to UniProtKB:  P56524
PHAROS:  P56524 GTEx:  ENSG00000068024

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OTF	C [auth A], G [auth B]	(1S,2S,3S)-1-fluoranyl-2-[4-(5-fluoranylpyrimidin-2-yl)phenyl]-N-oxidanyl-3-phenyl-cyclopropane-1-carboxamide C20 H15 F2 N3 O2 MREATSZIGJDNKB-HLIPFELVSA-N
ZN	D [auth A], E [auth A], H [auth B], I [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
NA	F [auth A], J [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
OTF	BindingDB:  5A2S	Kd: 20 (nM) from 1 assay(s)
		IC50: min: 10, max: 100 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free:  0.256 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.948	α = 90
b = 82.141	β = 90
c = 161.626	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-02-10 
Deposition Author(s): Luckhurst, C.A., Breccia, P., Stott, A.J., Aziz, O., Birch, H., Burli, R.W., Hughes, S., Jarvis, R.E., Lamers, M., Leonard, P., Matthews, K.L., McAllister, G., Pollack, S., Saville-Stones, E., Wishart, G., Yates, D., Dominguez, C.

Revision History  

• Version 1.0: 2016-02-10
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description