3SL6

Crystal structure of the catalytic domain of PDE4D2 with compound 12c

PDB DOI: https://doi.org/10.2210/pdb3SL6/pdb

Classification: Hydrolase/Hydrolase Inhibitor
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: 2.44 Å
R-Value Free: 0.256
R-Value Work: 0.198
R-Value Observed: 0.201

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 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: 170.64 kDa
Atom Count: 11,042
Modelled Residue Count: 1,301
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: 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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
JN8 Query on JN8 Download Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain HA [auth C] SDF format, chain V [auth B] SDF format, chain VA [auth D] MOL2 format, chain N [auth A] MOL2 format, chain HA [auth C] MOL2 format, chain V [auth B] MOL2 format, chain VA [auth D]	HA [auth C], N [auth A], V [auth B], VA [auth D]	cyclopentyl 6-(ethylcarbamoyl)-2-[(thiophen-2-ylacetyl)amino]-4,5,6,7-tetrahydrothieno[2,3-c]pyridine-3-carboxylate C₂₂ H₂₇ N₃ O₄ S₂ TWWIEHZKMVMPFQ-UHFFFAOYSA-N		Interactions Focus chain HA [auth C] Focus chain N [auth A] Focus chain V [auth B] Focus chain VA [auth D] Interactions & Density Focus chain HA [auth C] Focus chain N [auth A] Focus chain V [auth B] Focus chain VA [auth D]
EPE Query on EPE Download Ideal Coordinates CCD File SDF format, chain AA [auth C] MOL2 format, chain AA [auth C]	AA [auth C]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Interactions & Density Focus chain AA [auth C]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain W [auth B] MOL2 format, chain W [auth B]	W [auth B]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain W [auth B] Interactions & Density Focus chain W [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain JA [auth D] SDF format, chain KA [auth D] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain Y [auth C] SDF format, chain Z [auth C] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain KA [auth D] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C]	E [auth A] F [auth A] JA [auth D] KA [auth D] Q [auth B] E [auth A], F [auth A], JA [auth D], KA [auth D], Q [auth B], R [auth B], Y [auth C], Z [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain Q [auth B] Focus chain R [auth B] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain Q [auth B] Focus chain R [auth B] Focus chain Y [auth C] Focus chain Z [auth C]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain L [auth A] SDF format, chain UA [auth D] SDF format, chain BA [auth C] SDF format, chain EA [auth C] SDF format, chain FA [auth C] SDF format, chain GA [auth C] SDF format, chain I [auth A] SDF format, chain IA [auth D] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain LA [auth D] SDF format, chain M [auth A] SDF format, chain MA [auth D] SDF format, chain NA [auth D] SDF format, chain O [auth A] SDF format, chain OA [auth D] SDF format, chain P [auth A] SDF format, chain PA [auth D] SDF format, chain QA [auth D] SDF format, chain RA [auth D] SDF format, chain S [auth B] SDF format, chain SA [auth D] SDF format, chain T [auth B] SDF format, chain TA [auth D] SDF format, chain U [auth B] SDF format, chain X [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain L [auth A] MOL2 format, chain UA [auth D] MOL2 format, chain BA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain LA [auth D] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth D] MOL2 format, chain NA [auth D] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth D] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth D] MOL2 format, chain QA [auth D] MOL2 format, chain RA [auth D] MOL2 format, chain S [auth B] MOL2 format, chain SA [auth D] MOL2 format, chain T [auth B] MOL2 format, chain TA [auth D] MOL2 format, chain U [auth B] MOL2 format, chain X [auth C]	BA [auth C] CA [auth C] DA [auth C] EA [auth C] FA [auth C] BA [auth C], CA [auth C], DA [auth C], EA [auth C], FA [auth C], G [auth A], GA [auth C], H [auth A], I [auth A], IA [auth D], J [auth A], K [auth A], L [auth A], LA [auth D], M [auth A], MA [auth D], NA [auth D], O [auth A], OA [auth D], P [auth A], PA [auth D], QA [auth D], RA [auth D], S [auth B], SA [auth D], T [auth B], TA [auth D], U [auth B], UA [auth D], X [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain G [auth A] Focus chain GA [auth C] Focus chain H [auth A] Focus chain I [auth A] Focus chain IA [auth D] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth D] Focus chain M [auth A] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain O [auth A] Focus chain OA [auth D] Focus chain P [auth A] Focus chain PA [auth D] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain S [auth B] Focus chain SA [auth D] Focus chain T [auth B] Focus chain TA [auth D] Focus chain U [auth B] Focus chain UA [auth D] Focus chain X [auth C] Interactions & Density Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain G [auth A] Focus chain GA [auth C] Focus chain H [auth A] Focus chain I [auth A] Focus chain IA [auth D] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth D] Focus chain M [auth A] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain O [auth A] Focus chain OA [auth D] Focus chain P [auth A] Focus chain PA [auth D] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain S [auth B] Focus chain SA [auth D] Focus chain T [auth B] Focus chain TA [auth D] Focus chain U [auth B] Focus chain UA [auth D] Focus chain X [auth C]

Binding Affinity Annotations
ID	Source	Binding Affinity
JN8	Binding MOAD: 3SL6	IC50: 290 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.44 Å
R-Value Free: 0.256
R-Value Work: 0.198
R-Value Observed: 0.201
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.54	α = 90
b = 111.2	β = 90
c = 160.95	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data scaling
d*TREK	data reduction
PHENIX	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
MOLREP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

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: 2024-02-28
Changes: Data collection, Database references, Derived calculations