3SL3

Crystal structure of the apo form of the catalytic domain of PDE4D2

PDB DOI: https://doi.org/10.2210/pdb3SL3/pdb

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

Deposited: 2011-06-24 Released: 2011-10-26
Deposition Author(s): Feil, S.F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.252
R-Value Work: 0.205
R-Value Observed: 0.207

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Thiophene inhibitors of PDE4: Crystal structures show a second binding mode at the catalytic domain of PDE4D2.

Nankervis, J.L., Feil, S.C., Hancock, N.C., Zheng, Z., Ng, H.L., Morton, C.J., Holien, J.K., Ho, P.W., Frazzetto, M.M., Jennings, I.G., Manallack, D.T., Martin, T.J., Thompson, P.E., Parker, M.W.

(2011) Bioorg Med Chem Lett 21: 7089-7093

PubMed: 22030030 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2011.09.109
Primary Citation of Related Structures:
3SL3, 3SL4, 3SL5, 3SL6, 3SL8

PubMed Abstract:
PDE4 inhibitors have been identified as therapeutic targets for a variety of conditions, particularly inflammatory diseases. We have serendipitously identified a novel class of phosphodiesterase 4 (PDE4) inhibitor during a study to discover antagonists of the parathyroid hormone receptor. X-ray crystallographic studies of PDE4D2 complexed to four potent inhibitors reveal the atomic details of how they inhibit the enzyme and a notable contrast to another recently reported thiophene-based inhibitor.

Organizational Affiliation

Medicinal Chemistry & Drug Action, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville campus), Parkville, Victoria, Australia.

Macromolecule Content

Total Structure Weight: 171.78 kDa
Atom Count: 11,280
Modelled Residue Count: 1,295
Deposited Residue Count: 1,444
Unique protein chains: 1

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	A, B, C, D	361	Homo sapiens	Mutation(s): 0 Gene Names: DPDE3, PDE4D 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 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPE Query on EPE Download Ideal Coordinates CCD File SDF format, chain UA [auth C] MOL2 format, chain UA [auth C]	UA [auth C]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain UA [auth C] Interactions & Density Focus chain UA [auth C]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain PA [auth B] SDF format, chain TB [auth D] SDF format, chain R [auth A] SDF format, chain RB [auth D] MOL2 format, chain PA [auth B] MOL2 format, chain TB [auth D] MOL2 format, chain R [auth A] MOL2 format, chain RB [auth D]	PA [auth B], R [auth A], RB [auth D], TB [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain PA [auth B] Focus chain R [auth A] Focus chain RB [auth D] Focus chain TB [auth D] Interactions & Density Focus chain PA [auth B] Focus chain R [auth A] Focus chain RB [auth D] Focus chain TB [auth D]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain BC [auth D] SDF format, chain FB [auth C] SDF format, chain U [auth A] SDF format, chain JA [auth B] MOL2 format, chain BC [auth D] MOL2 format, chain FB [auth C] MOL2 format, chain U [auth A] MOL2 format, chain JA [auth B]	BC [auth D], FB [auth C], JA [auth B], U [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain BC [auth D] Focus chain FB [auth C] Focus chain JA [auth B] Focus chain U [auth A] Interactions & Density Focus chain BC [auth D] Focus chain FB [auth C] Focus chain JA [auth B] Focus chain U [auth A]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain IB [auth D] SDF format, chain MA [auth B] SDF format, chain NA [auth B] SDF format, chain NB [auth D] SDF format, chain VA [auth C] MOL2 format, chain IB [auth D] MOL2 format, chain MA [auth B] MOL2 format, chain NA [auth B] MOL2 format, chain NB [auth D] MOL2 format, chain VA [auth C]	IB [auth D], MA [auth B], NA [auth B], NB [auth D], VA [auth C]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain IB [auth D] Focus chain MA [auth B] Focus chain NA [auth B] Focus chain NB [auth D] Focus chain VA [auth C] Interactions & Density Focus chain IB [auth D] Focus chain MA [auth B] Focus chain NA [auth B] Focus chain NB [auth D] Focus chain VA [auth C]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain AC [auth D] SDF format, chain DB [auth C] SDF format, chain EB [auth C] SDF format, chain HA [auth B] SDF format, chain S [auth A] SDF format, chain ZB [auth D] SDF format, chain IA [auth B] SDF format, chain T [auth A] MOL2 format, chain AC [auth D] MOL2 format, chain DB [auth C] MOL2 format, chain EB [auth C] MOL2 format, chain HA [auth B] MOL2 format, chain S [auth A] MOL2 format, chain ZB [auth D] MOL2 format, chain IA [auth B] MOL2 format, chain T [auth A]	AC [auth D] DB [auth C] EB [auth C] HA [auth B] IA [auth B] AC [auth D], DB [auth C], EB [auth C], HA [auth B], IA [auth B], S [auth A], T [auth A], ZB [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AC [auth D] Focus chain DB [auth C] Focus chain EB [auth C] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain S [auth A] Focus chain T [auth A] Focus chain ZB [auth D] Interactions & Density Focus chain AC [auth D] Focus chain DB [auth C] Focus chain EB [auth C] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain S [auth A] Focus chain T [auth A] Focus chain ZB [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain AB [auth C] SDF format, chain BA [auth B] SDF format, chain BB [auth C] SDF format, chain CC [auth D] SDF format, chain DA [auth B] SDF format, chain DC [auth D] SDF format, chain E [auth A] SDF format, chain EA [auth B] SDF format, chain EC [auth D] SDF format, chain F [auth A] SDF format, chain FC [auth D] SDF format, chain G [auth A] SDF format, chain GB [auth C] SDF format, chain GC [auth D] SDF format, chain H [auth A] SDF format, chain HC [auth D] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain JB [auth D] SDF format, chain KA [auth B] SDF format, chain L [auth A] SDF format, chain LA [auth B] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain PB [auth D] SDF format, chain Q [auth A] SDF format, chain QA [auth C] SDF format, chain SA [auth C] SDF format, chain UB [auth D] SDF format, chain V [auth A] SDF format, chain VB [auth D] SDF format, chain W [auth A] SDF format, chain WA [auth C] SDF format, chain XA [auth C] SDF format, chain XB [auth D] SDF format, chain YA [auth C] SDF format, chain Z [auth B] SDF format, chain CA [auth B] SDF format, chain CB [auth C] SDF format, chain FA [auth B] SDF format, chain GA [auth B] SDF format, chain HB [auth D] SDF format, chain K [auth A] SDF format, chain KB [auth D] SDF format, chain LB [auth D] SDF format, chain MB [auth D] SDF format, chain OA [auth B] SDF format, chain OB [auth D] SDF format, chain P [auth A] SDF format, chain QB [auth D] SDF format, chain RA [auth C] SDF format, chain SB [auth D] SDF format, chain TA [auth C] SDF format, chain WB [auth D] SDF format, chain X [auth A] SDF format, chain Y [auth A] SDF format, chain YB [auth D] SDF format, chain ZA [auth C] MOL2 format, chain AA [auth B] MOL2 format, chain AB [auth C] MOL2 format, chain BA [auth B] MOL2 format, chain BB [auth C] MOL2 format, chain CC [auth D] MOL2 format, chain DA [auth B] MOL2 format, chain DC [auth D] MOL2 format, chain E [auth A] MOL2 format, chain EA [auth B] MOL2 format, chain EC [auth D] MOL2 format, chain F [auth A] MOL2 format, chain FC [auth D] MOL2 format, chain G [auth A] MOL2 format, chain GB [auth C] MOL2 format, chain GC [auth D] MOL2 format, chain H [auth A] MOL2 format, chain HC [auth D] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain JB [auth D] MOL2 format, chain KA [auth B] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth B] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain PB [auth D] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth C] MOL2 format, chain SA [auth C] MOL2 format, chain UB [auth D] MOL2 format, chain V [auth A] MOL2 format, chain VB [auth D] MOL2 format, chain W [auth A] MOL2 format, chain WA [auth C] MOL2 format, chain XA [auth C] MOL2 format, chain XB [auth D] MOL2 format, chain YA [auth C] MOL2 format, chain Z [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain CB [auth C] MOL2 format, chain FA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain HB [auth D] MOL2 format, chain K [auth A] MOL2 format, chain KB [auth D] MOL2 format, chain LB [auth D] MOL2 format, chain MB [auth D] MOL2 format, chain OA [auth B] MOL2 format, chain OB [auth D] MOL2 format, chain P [auth A] MOL2 format, chain QB [auth D] MOL2 format, chain RA [auth C] MOL2 format, chain SB [auth D] MOL2 format, chain TA [auth C] MOL2 format, chain WB [auth D] MOL2 format, chain X [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain YB [auth D] MOL2 format, chain ZA [auth C]	AA [auth B] AB [auth C] BA [auth B] BB [auth C] CA [auth B] AA [auth B], AB [auth C], BA [auth B], BB [auth C], CA [auth B], CB [auth C], CC [auth D], DA [auth B], DC [auth D], E [auth A], EA [auth B], EC [auth D], F [auth A], FA [auth B], FC [auth D], G [auth A], GA [auth B], GB [auth C], GC [auth D], H [auth A], HB [auth D], HC [auth D], I [auth A], J [auth A], JB [auth D], K [auth A], KA [auth B], KB [auth D], L [auth A], LA [auth B], LB [auth D], M [auth A], MB [auth D], N [auth A], O [auth A], OA [auth B], OB [auth D], P [auth A], PB [auth D], Q [auth A], QA [auth C], QB [auth D], RA [auth C], SA [auth C], SB [auth D], TA [auth C], UB [auth D], V [auth A], VB [auth D], W [auth A], WA [auth C], WB [auth D], X [auth A], XA [auth C], XB [auth D], Y [auth A], YA [auth C], YB [auth D], Z [auth B], ZA [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain AB [auth C] Focus chain BA [auth B] Focus chain BB [auth C] Focus chain CA [auth B] Focus chain CB [auth C] Focus chain CC [auth D] Focus chain DA [auth B] Focus chain DC [auth D] Focus chain E [auth A] Focus chain EA [auth B] Focus chain EC [auth D] Focus chain F [auth A] Focus chain FA [auth B] Focus chain FC [auth D] Focus chain G [auth A] Focus chain GA [auth B] Focus chain GB [auth C] Focus chain GC [auth D] Focus chain H [auth A] Focus chain HB [auth D] Focus chain HC [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain JB [auth D] Focus chain K [auth A] Focus chain KA [auth B] Focus chain KB [auth D] Focus chain L [auth A] Focus chain LA [auth B] Focus chain LB [auth D] Focus chain M [auth A] Focus chain MB [auth D] Focus chain N [auth A] Focus chain O [auth A] Focus chain OA [auth B] Focus chain OB [auth D] Focus chain P [auth A] Focus chain PB [auth D] Focus chain Q [auth A] Focus chain QA [auth C] Focus chain QB [auth D] Focus chain RA [auth C] Focus chain SA [auth C] Focus chain SB [auth D] Focus chain TA [auth C] Focus chain UB [auth D] Focus chain V [auth A] Focus chain VB [auth D] Focus chain W [auth A] Focus chain WA [auth C] Focus chain WB [auth D] Focus chain X [auth A] Focus chain XA [auth C] Focus chain XB [auth D] Focus chain Y [auth A] Focus chain YA [auth C] Focus chain YB [auth D] Focus chain Z [auth B] Focus chain ZA [auth C] Interactions & Density Focus chain AA [auth B] Focus chain AB [auth C] Focus chain BA [auth B] Focus chain BB [auth C] Focus chain CA [auth B] Focus chain CB [auth C] Focus chain CC [auth D] Focus chain DA [auth B] Focus chain DC [auth D] Focus chain E [auth A] Focus chain EA [auth B] Focus chain EC [auth D] Focus chain F [auth A] Focus chain FA [auth B] Focus chain FC [auth D] Focus chain G [auth A] Focus chain GA [auth B] Focus chain GB [auth C] Focus chain GC [auth D] Focus chain H [auth A] Focus chain HB [auth D] Focus chain HC [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain JB [auth D] Focus chain K [auth A] Focus chain KA [auth B] Focus chain KB [auth D] Focus chain L [auth A] Focus chain LA [auth B] Focus chain LB [auth D] Focus chain M [auth A] Focus chain MB [auth D] Focus chain N [auth A] Focus chain O [auth A] Focus chain OA [auth B] Focus chain OB [auth D] Focus chain P [auth A] Focus chain PB [auth D] Focus chain Q [auth A] Focus chain QA [auth C] Focus chain QB [auth D] Focus chain RA [auth C] Focus chain SA [auth C] Focus chain SB [auth D] Focus chain TA [auth C] Focus chain UB [auth D] Focus chain V [auth A] Focus chain VB [auth D] Focus chain W [auth A] Focus chain WA [auth C] Focus chain WB [auth D] Focus chain X [auth A] Focus chain XA [auth C] Focus chain XB [auth D] Focus chain Y [auth A] Focus chain YA [auth C] Focus chain YB [auth D] Focus chain Z [auth B] Focus chain ZA [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.252
R-Value Work: 0.205
R-Value Observed: 0.207
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.269	α = 90
b = 111.757	β = 90
c = 160.279	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2011-10-26

Deposition Author(s):

Feil, S.F.

Revision History (Full details and data files)

Version 1.0: 2011-10-26
Type: Initial release
Version 1.1: 2011-12-14
Changes: Database references
Version 1.2: 2017-11-08
Changes: Advisory, Refinement description
Version 1.3: 2024-02-28
Changes: Advisory, Data collection, Database references, Derived calculations