3O0J

PDE4B In complex with ligand an2898

• PDB DOI: https://doi.org/10.2210/pdb3O0J/pdb

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


• Deposited: 2010-07-19 Released: 2011-08-10 
• Deposition Author(s): Alley, M.R.K., Zhou, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.236 
• R-Value Work: 0.184 
• R-Value Observed: 0.187 

Literature

Boron-based phosphodiesterase inhibitors show novel binding of boron to PDE4 bimetal center.

Freund, Y.R., Akama, T., Alley, M.R., Antunes, J., Dong, C., Jarnagin, K., Kimura, R., Nieman, J.A., Maples, K.R., Plattner, J.J., Rock, F., Sharma, R., Singh, R., Sanders, V., Zhou, Y.

(2012) FEBS Lett 586: 3410-3414

• PubMed: 22841723 
• DOI: https://doi.org/10.1016/j.febslet.2012.07.058
• Primary Citation of Related Structures:  
  3O0J


• PubMed Abstract: 
  

  We have used boron-based molecules to create novel, competitive, reversible inhibitors of phosphodiesterase 4 (PDE4). The co-crystal structure reveals a binding configuration which is unique compared to classical catechol PDE4 inhibitors, with boron binding to the activated water in the bimetal center. These phenoxybenzoxaboroles can be optimized to generate submicromolar potency enzyme inhibitors, which inhibit TNF-α, IL-2, IFN-γ, IL-5 and IL-10 activities in vitro and show safety and efficacy for topical treatment of human psoriasis. They provide a valuable new route for creating novel potent anti-PDE4 inhibitors.

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Organizational Affiliation: 

Anacor Pharmaceuticals Inc., Palo Alto, CA 94303, USA. [e-mail]

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 38.55 kDa 
• Atom Count: 2,896 
• Modelled Residue Count: 323 
• Deposited Residue Count: 323 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cAMP-specific 3',5'-cyclic phosphodiesterase 4B	A	323	Homo sapiens	Mutation(s): 0  EC: 3.1.4.17
UniProt & NIH Common Fund Data Resources
Find proteins for Q07343 (Homo sapiens) Explore Q07343  Go to UniProtKB:  Q07343
PHAROS:  Q07343 GTEx:  ENSG00000184588

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3OJ	D [auth A]	4-[(1-hydroxy-1,3-dihydro-2,1-benzoxaborol-5-yl)oxy]benzene-1,2-dicarbonitrile C15 H9 B N2 O3 UBMGTTRDNUKZMT-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
3OJ	PDBBind:  3O0J	Ki: 65 (nM) from 1 assay(s)
	BindingDB:  3O0J	IC50: min: 60, max: 240 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.236 
• R-Value Work: 0.184 
• R-Value Observed: 0.187 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.611	α = 90
b = 53.611	β = 90
c = 229.014	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-08-10 
Deposition Author(s): Alley, M.R.K., Zhou, Y.

Revision History  

• Version 1.0: 2011-08-10
  Type: Initial release
  
• Version 1.1: 2011-11-30
  Changes: Structure summary
• Version 1.2: 2013-01-23
  Changes: Database references
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references, Derived calculations