3I8V | pdb_00003i8v

Crystal structure of human PDE4a with 4-(3-butoxy-4-methoxyphenyl)methyl-2-imidazolidone

• PDB DOI: https://doi.org/10.2210/pdb3I8V/pdb

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


• Deposited: 2009-07-10 Released: 2009-07-21 
• Deposition Author(s): Cheng, R.K.Y., Crawley, L., Barker, J., Wood, M., Felicetti, B., Whittaker, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.222 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of human PDE4a with 4-(3-butoxy-4-methoxyphenyl)methyl-2-imidazolidone

Cheng, R.K.Y., Crawley, L., Barker, J., Wood, M., Felicetti, B., Whittaker, M.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 82.45 kDa 
• Atom Count: 5,833 
• Modeled Residue Count: 669 
• Deposited Residue Count: 708 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cAMP-specific 3',5'-cyclic phosphodiesterase 4A	A, B	354	Homo sapiens	Mutation(s): 0  Gene Names: PDE4A, DPDE2 EC: 3.1.4.17 (PDB Primary Data), 3.1.4.53 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P27815 (Homo sapiens) Explore P27815  Go to UniProtKB:  P27815
PHAROS:  P27815 GTEx:  ENSG00000065989

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0MO	E [auth A], J [auth B]	(4R)-4-(3-butoxy-4-methoxybenzyl)imidazolidin-2-one C15 H22 N2 O3 PDMUULPVBYQBBK-GFCCVEGCSA-N
GOL	F [auth A], K [auth B], L [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	C [auth A], H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CO	G [auth A]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N
MG	D [auth A], I [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSS	A, B	L-PEPTIDE LINKING	C3 H7 N O2 S2		CYS

Binding Affinity Annotations
ID	Source	Binding Affinity
0MO	BindingDB:  3I8V	Ki: min: 189.1, max: 1.00e+4 (nM) from 3 assay(s)
		IC50: min: 4300, max: 2.60e+4 (nM) from 3 assay(s)
		EC50: 3300 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.222 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.406	α = 90
b = 105.406	β = 90
c = 165.252	γ = 90

Software Package:

Software Name	Purpose
DNA	data collection
PHASER	phasing
REFMAC	refinement
CrystalClear	data reduction
CrystalClear	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-07-21 
Deposition Author(s): Cheng, R.K.Y., Crawley, L., Barker, J., Wood, M., Felicetti, B., Whittaker, M.

Revision History  

• Version 1.0: 2009-07-21
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2023-11-22
  Changes: Data collection
• Version 1.4: 2024-11-20
  Changes: Structure summary