3SL8

Crystal structure of the catalytic domain of PDE4D2 with compound 10o

PDB DOI: https://doi.org/10.2210/pdb3SL8/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: 2.60 Å
R-Value Free: 0.273
R-Value Work: 0.196
R-Value Observed: 0.200

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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: 170.88 kDa
Atom Count: 11,046
Modelled Residue Count: 1,299
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 (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 Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
JN7 Query on JN7 Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain T [auth A] SDF format, chain ZA [auth D] SDF format, chain IA [auth C] MOL2 format, chain AA [auth B] MOL2 format, chain T [auth A] MOL2 format, chain ZA [auth D] MOL2 format, chain IA [auth C] mmCIF format, chain AA [auth B] mmCIF format, chain T [auth A] mmCIF format, chain ZA [auth D] mmCIF format, chain IA [auth C]	AA [auth B], IA [auth C], T [auth A], ZA [auth D]	3-cyclopentyl 6-ethenyl 2-[(thiophen-2-ylacetyl)amino]-4,7-dihydrothieno[2,3-c]pyridine-3,6(5H)-dicarboxylate C₂₂ H₂₄ N₂ O₅ S₂ RIZICIJVRFSMJP-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain IA [auth C] Focus chain T [auth A] Focus chain ZA [auth D] Interactions & Density Focus chain AA [auth B] Focus chain IA [auth C] Focus chain T [auth A] Focus chain ZA [auth D]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain OA [auth D] MOL2 format, chain N [auth A] MOL2 format, chain OA [auth D] mmCIF format, chain N [auth A] mmCIF format, chain OA [auth D]	N [auth A], OA [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Focus chain OA [auth D] Interactions & Density Focus chain N [auth A] Focus chain OA [auth D]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain GA [auth C] SDF format, chain X [auth B] MOL2 format, chain GA [auth C] MOL2 format, chain X [auth B] mmCIF format, chain GA [auth C] mmCIF format, chain X [auth B]	GA [auth C], X [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain GA [auth C] Focus chain X [auth B] Interactions & Density Focus chain GA [auth C] Focus chain X [auth B]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain HA [auth C] SDF format, chain XA [auth D] MOL2 format, chain HA [auth C] MOL2 format, chain XA [auth D] mmCIF format, chain HA [auth C] mmCIF format, chain XA [auth D]	HA [auth C], XA [auth D]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain HA [auth C] Focus chain XA [auth D] Interactions & Density Focus chain HA [auth C] Focus chain XA [auth D]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain EA [auth C] SDF format, chain F [auth A] SDF format, chain FA [auth C] SDF format, chain G [auth A] SDF format, chain PA [auth D] SDF format, chain V [auth B] SDF format, chain QA [auth D] SDF format, chain W [auth B] MOL2 format, chain EA [auth C] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth C] MOL2 format, chain G [auth A] MOL2 format, chain PA [auth D] MOL2 format, chain V [auth B] MOL2 format, chain QA [auth D] MOL2 format, chain W [auth B] mmCIF format, chain EA [auth C] mmCIF format, chain F [auth A] mmCIF format, chain FA [auth C] mmCIF format, chain G [auth A] mmCIF format, chain PA [auth D] mmCIF format, chain V [auth B] mmCIF format, chain QA [auth D] mmCIF format, chain W [auth B]	EA [auth C] F [auth A] FA [auth C] G [auth A] PA [auth D] EA [auth C], F [auth A], FA [auth C], G [auth A], PA [auth D], QA [auth D], V [auth B], W [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain EA [auth C] Focus chain F [auth A] Focus chain FA [auth C] Focus chain G [auth A] Focus chain PA [auth D] Focus chain QA [auth D] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain EA [auth C] Focus chain F [auth A] Focus chain FA [auth C] Focus chain G [auth A] Focus chain PA [auth D] Focus chain QA [auth D] Focus chain V [auth B] Focus chain W [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain E [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain JA [auth D] SDF format, chain K [auth A] SDF format, chain KA [auth D] SDF format, chain L [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 P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain RA [auth D] SDF format, chain SA [auth D] SDF format, chain TA [auth D] SDF format, chain U [auth A] SDF format, chain UA [auth D] SDF format, chain VA [auth D] SDF format, chain WA [auth D] SDF format, chain Y [auth B] SDF format, chain YA [auth D] SDF format, chain Z [auth B] SDF format, chain BA [auth C] SDF format, chain S [auth A] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain E [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain L [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 P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth D] MOL2 format, chain SA [auth D] MOL2 format, chain TA [auth D] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth D] MOL2 format, chain VA [auth D] MOL2 format, chain WA [auth D] MOL2 format, chain Y [auth B] MOL2 format, chain YA [auth D] MOL2 format, chain Z [auth B] MOL2 format, chain BA [auth C] MOL2 format, chain S [auth A] mmCIF format, chain CA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain E [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth D] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth D] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth D] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth D] mmCIF format, chain NA [auth D] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain RA [auth D] mmCIF format, chain SA [auth D] mmCIF format, chain TA [auth D] mmCIF format, chain U [auth A] mmCIF format, chain UA [auth D] mmCIF format, chain VA [auth D] mmCIF format, chain WA [auth D] mmCIF format, chain Y [auth B] mmCIF format, chain YA [auth D] mmCIF format, chain Z [auth B] mmCIF format, chain BA [auth C] mmCIF format, chain S [auth A]	BA [auth C] CA [auth C] DA [auth C] E [auth A] H [auth A] BA [auth C], CA [auth C], DA [auth C], E [auth A], H [auth A], I [auth A], J [auth A], JA [auth D], K [auth A], KA [auth D], L [auth A], LA [auth D], M [auth A], MA [auth D], NA [auth D], O [auth A], P [auth A], Q [auth A], R [auth A], RA [auth D], S [auth A], SA [auth D], TA [auth D], U [auth A], UA [auth D], VA [auth D], WA [auth D], Y [auth B], YA [auth D], Z [auth B]	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 E [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain JA [auth D] Focus chain K [auth A] Focus chain KA [auth D] 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 P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain RA [auth D] Focus chain S [auth A] Focus chain SA [auth D] Focus chain TA [auth D] Focus chain U [auth A] Focus chain UA [auth D] Focus chain VA [auth D] Focus chain WA [auth D] Focus chain Y [auth B] Focus chain YA [auth D] Focus chain Z [auth B] Interactions & Density Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain E [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain JA [auth D] Focus chain K [auth A] Focus chain KA [auth D] 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 P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain RA [auth D] Focus chain S [auth A] Focus chain SA [auth D] Focus chain TA [auth D] Focus chain U [auth A] Focus chain UA [auth D] Focus chain VA [auth D] Focus chain WA [auth D] Focus chain Y [auth B] Focus chain YA [auth D] Focus chain Z [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
JN7	PDBBind: 3SL8	IC50: 290 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.273
R-Value Work: 0.196
R-Value Observed: 0.200
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.14	α = 90
b = 111.65	β = 90
c = 161.74	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
XDS	data reduction
XDS	data scaling
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: 2017-11-08
Changes: Refinement description
Version 1.3: 2024-02-28
Changes: Data collection, Database references, Derived calculations