Download MendeleyThe 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.
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
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
Starting Model: experimental
View more details
This is version 1.2 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 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 GTEx: ENSG00000113448 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q08499 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| 0MO Query on 0MO | C [auth A] | (4R)-4-(3-butoxy-4-methoxybenzyl)imidazolidin-2-one C15 H22 N2 O3 PDMUULPVBYQBBK-GFCCVEGCSA-N |  | ||
| ZN Query on ZN | B [auth A] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | ||
| MG Query on MG | D [auth A] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
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 Name | Purpose |
|---|---|
| DNA | data collection |
| PHASER | phasing |
| REFMAC | refinement |
| CrystalClear | data reduction |
| CrystalClear | data scaling |
Entry History
Deposition Data
- Released Date: 2009-10-20 Deposition Author(s): Crawley, L., Cheng, R.K.Y., Wood, M., Barker, J., Felicetti, B., Whittaker, M.
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
