3K4S

The structure of the catalytic domain of human PDE4d with 4-(3-Butoxy-4-methoxyphenyl)methyl-2-imidazolidone

PDB DOI: https://doi.org/10.2210/pdb3K4S/pdb

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

Deposited: 2009-10-06 Released: 2009-10-20
Deposition Author(s): Crawley, L., Cheng, R.K.Y., Wood, M., Barker, J., Felicetti, B., Whittaker, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.262
R-Value Work: 0.209
R-Value Observed: 0.211

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

The structure of the catalytic domain of human PDE4d with 4-(3-Butoxy-4-methoxyphenyl)methyl-2-imidazolidone

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

To be published.

Macromolecule Content

Total Structure Weight: 40.46 kDa
Atom Count: 2,985
Modelled Residue Count: 329
Deposited Residue Count: 349
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cAMP-specific 3',5'-cyclic phosphodiesterase 4D	A	349	Homo sapiens	Mutation(s): 0 Gene Names: PDE4D, DPDE3 EC: 3.1.4.17
UniProt & NIH Common Fund Data Resources
Find proteins for Q08499 (Homo sapiens) Explore Q08499 Go to UniProtKB: Q08499
PHAROS: Q08499 GTEx: ENSG00000113448
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q08499
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
0MO Query on 0MO Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	(4R)-4-(3-butoxy-4-methoxybenzyl)imidazolidin-2-one C₁₅ H₂₂ N₂ O₃ PDMUULPVBYQBBK-GFCCVEGCSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
0MO	BindingDB: 3K4S	IC50: min: 4800, max: 2.60e+4 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.262
R-Value Work: 0.209
R-Value Observed: 0.211
Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.217	α = 90
b = 83.217	β = 90
c = 148.766	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2009-10-20

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-10-20
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description

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Help and Resources

3K4S

The structure of the catalytic domain of human PDE4d with 4-(3-Butoxy-4-methoxyphenyl)methyl-2-imidazolidone

The structure of the catalytic domain of human PDE4d with 4-(3-Butoxy-4-methoxyphenyl)methyl-2-imidazolidone

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)