Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 82.69 kDa 
• Atom Count: 6,011 
• Modelled Residue Count: 652 
• Deposited Residue Count: 698 
• Unique protein chains: 1

 1Y2D

Catalytic Domain Of Human Phosphodiesterase 4D In Complex With 1-(4-methoxy-phenyl)-3,5-dimethyl-1H-pyrazole-4-carboxylic acid ethyl ester

• PDB DOI:  https://doi.org/10.2210/pdb1Y2D/pdb

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


• Deposited: 2004-11-22 Released: 2005-03-01 
• Deposition Author(s): Card, G.L., Blasdel, L., England, B.P., Zhang, C., Suzuki, Y., Gillette, S., Fong, D., Ibrahim, P.N., Artis, D.R., Bollag, G., Milburn, M.V., Kim, S.-H., Schlessinger, J., Zhang, K.Y.J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.189 
• R-Value Work: 0.165 
• R-Value Observed: 0.166 

Literature

A family of phosphodiesterase inhibitors discovered by cocrystallography and scaffold-based drug design

Card, G.L., Blasdel, L., England, B.P., Zhang, C., Suzuki, Y., Gillette, S., Fong, D., Ibrahim, P.N., Artis, D.R., Bollag, G., Milburn, M.V., Kim, S.-H., Schlessinger, J., Zhang, K.Y.J.

(2005) Nat Biotechnol 23: 201-207

• PubMed: 15685167 
• DOI: https://doi.org/10.1038/nbt1059
• Primary Citation of Related Structures:  
  1Y2B, 1Y2C, 1Y2D, 1Y2E, 1Y2H, 1Y2J, 1Y2K


• PubMed Abstract: 
  

Cyclic nucleotide phosphodiesterases (PDEs) comprise a large family of enzymes that regulate a variety of cellular processes. We describe a family of potent PDE4 inhibitors discovered using an efficient method for scaffold-based drug design. This method involves an iterative approach starting with low-affinity screening of compounds followed by high-throughput cocrystallography to reveal the molecular basis underlying the activity of the newly identified compounds. Through detailed structural analysis of the interaction of the initially discovered pyrazole carboxylic ester scaffold with PDE4D using X-ray crystallography, we identified three sites of chemical substitution and designed small selective libraries of scaffold derivatives with modifications at these sites. A 4,000-fold increase in the potency of this PDE4 inhibitor was achieved after only two rounds of chemical synthesis and the structural analysis of seven pyrazole derivatives bound to PDE4B or PDE4D, revealing the robustness of this approach for identifying new inhibitors that can be further developed into drug candidates.

---

Organizational Affiliation: 

Plexxikon Inc., 91 Bolivar Dr., Berkeley, California 94710, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cAMP-specific 3',5'-cyclic phosphodiesterase 4D	A, B	349	Homo sapiens	Mutation(s): 0  Gene Names: PDE4D, DPDE3 EC: 3.1.4.17 (PDB Primary Data), 3.1.4.53 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q08499 (Homo sapiens) Explore Q08499  Go to UniProtKB:  Q08499
PHAROS:  Q08499

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
B3P	GA [auth B]	2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C11 H26 N2 O6 HHKZCCWKTZRCCL-UHFFFAOYSA-N
4DE	E [auth A], T [auth B]	1-(4-METHOXYPHENYL)-3,5-DIMETHYL-1H-PYRAZOLE-4-CARBOXYLIC ACID ETHYL ESTER C15 H18 N2 O3 ZDSXCFSUGVAQSB-UHFFFAOYSA-N
ZN	C [auth A], R [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	AA [auth B], BA [auth B], CA [auth B], DA [auth B], EA [auth B], F [auth A], FA [auth B], 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], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG	D [auth A], S [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
4DE	BindingDB:  1Y2D	IC50: min: 2000, max: 2000 (nM) from 2 assay(s)
	PDBBind:  1Y2D	IC50: 2000 (nM) from 1 assay(s)
	Binding MOAD:  1Y2D	IC50: 2000 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.189 
• R-Value Work: 0.165 
• R-Value Observed: 0.166 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.804	α = 90
b = 79.146	β = 90
c = 164.617	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Blu-Ice	data collection
ELVES	data scaling
EPMR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-03-01 
Deposition Author(s): Card, G.L., Blasdel, L., England, B.P., Zhang, C., Suzuki, Y., Gillette, S., Fong, D., Ibrahim, P.N., Artis, D.R., Bollag, G., Milburn, M.V., Kim, S.-H., Schlessinger, J., Zhang, K.Y.J.

Revision History  

• Version 1.0: 2005-03-01
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance