4OGB | pdb_00004ogb

Crystal structure of the catalytic domain of PDE4D2 with compound 2

PDB DOI: https://doi.org/10.2210/pdb4OGB/pdb

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

Deposited: 2014-01-15 Released: 2015-01-21
Deposition Author(s): Feil, S.C., Parker, M.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.03 Å
R-Value Free:
0.243 (Depositor), 0.244 (DCC)
R-Value Work:
0.202 (Depositor), 0.206 (DCC)
R-Value Observed:
0.204 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

The PDE inhibition profile of LY294002 and tetrahydropyranyl analogues reveals a chromone motif for the development of PDE inhibitors

Howard, B.L., Nankervis, J.L., Feil, S.C., Manallack, D.T., Holien, J.K., Zhen, Z., Jennings, I.G., Abbott, B.M., Parker, M.W., Thompson, P.E.

To be published.

Macromolecule Content

Total Structure Weight: 171.27 kDa
Atom Count: 11,286
Modeled Residue Count: 1,298
Deposited Residue Count: 1,444
Unique protein chains: 1

Macromolecules

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| 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: 3.1.4.53
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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q08499
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
2SR Query on 2SR Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain FA [auth C] SDF format, chain S [auth B] SDF format, chain SA [auth D] MOL2 format, chain E [auth A] MOL2 format, chain FA [auth C] MOL2 format, chain S [auth B] MOL2 format, chain SA [auth D] mmCIF format, chain E [auth A] mmCIF format, chain FA [auth C] mmCIF format, chain S [auth B] mmCIF format, chain SA [auth D]	E [auth A], FA [auth C], S [auth B], SA [auth D]	(2R)-8-(3,4-dimethoxyphenyl)-6-methyl-2-(tetrahydro-2H-pyran-4-yl)-2H-chromen-4-ol C₂₃ H₂₆ O₅ RVKGQUJUMMUCKA-NRFANRHFSA-N		Interactions Focus chain E [auth A] Focus chain FA [auth C] Focus chain S [auth B] Focus chain SA [auth D] Interactions & Density Focus chain E [auth A] Focus chain FA [auth C] Focus chain S [auth B] Focus chain SA [auth D]
EPE Query on EPE Download:Ideal Coordinates CCD File SDF format, chain JA [auth C] MOL2 format, chain JA [auth C] mmCIF format, chain JA [auth C]	JA [auth C]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain JA [auth C] Interactions & Density Focus chain JA [auth C]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain FB [auth D] SDF format, chain GB [auth D] SDF format, chain H [auth A] SDF format, chain XA [auth D] MOL2 format, chain FB [auth D] MOL2 format, chain GB [auth D] MOL2 format, chain H [auth A] MOL2 format, chain XA [auth D] mmCIF format, chain FB [auth D] mmCIF format, chain GB [auth D] mmCIF format, chain H [auth A] mmCIF format, chain XA [auth D]	FB [auth D], GB [auth D], H [auth A], XA [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain FB [auth D] Focus chain GB [auth D] Focus chain H [auth A] Focus chain XA [auth D] Interactions & Density Focus chain FB [auth D] Focus chain GB [auth D] Focus chain H [auth A] Focus chain XA [auth D]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain DA [auth B] SDF format, chain O [auth A] SDF format, chain Q [auth A] SDF format, chain YA [auth D] SDF format, chain UA [auth D] SDF format, chain BA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain O [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain YA [auth D] MOL2 format, chain UA [auth D] MOL2 format, chain BA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain O [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain YA [auth D] mmCIF format, chain UA [auth D] mmCIF format, chain BA [auth B]	BA [auth B] DA [auth B] O [auth A] Q [auth A] UA [auth D] BA [auth B], DA [auth B], O [auth A], Q [auth A], UA [auth D], YA [auth D]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain BA [auth B] Focus chain DA [auth B] Focus chain O [auth A] Focus chain Q [auth A] Focus chain UA [auth D] Focus chain YA [auth D] Interactions & Density Focus chain BA [auth B] Focus chain DA [auth B] Focus chain O [auth A] Focus chain Q [auth A] Focus chain UA [auth D] Focus chain YA [auth D]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain CB [auth D] SDF format, chain DB [auth D] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain OA [auth C] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain NA [auth C] MOL2 format, chain CB [auth D] MOL2 format, chain DB [auth D] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain OA [auth C] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain NA [auth C] mmCIF format, chain CB [auth D] mmCIF format, chain DB [auth D] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain OA [auth C] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain NA [auth C]	CB [auth D] DB [auth D] M [auth A] N [auth A] NA [auth C] CB [auth D], DB [auth D], M [auth A], N [auth A], NA [auth C], OA [auth C], T [auth B], U [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain CB [auth D] Focus chain DB [auth D] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth C] Focus chain OA [auth C] Focus chain T [auth B] Focus chain U [auth B] Interactions & Density Focus chain CB [auth D] Focus chain DB [auth D] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth C] Focus chain OA [auth C] Focus chain T [auth B] Focus chain U [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain AB [auth D] SDF format, chain BB [auth D] SDF format, chain CA [auth B] SDF format, chain EA [auth C] SDF format, chain G [auth A] SDF format, chain GA [auth C] SDF format, chain HA [auth C] SDF format, chain I [auth A] SDF format, chain IA [auth C] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain KA [auth C] SDF format, chain L [auth A] SDF format, chain LA [auth C] SDF format, chain MA [auth C] SDF format, chain P [auth A] SDF format, chain PA [auth C] SDF format, chain QA [auth C] SDF format, chain R [auth A] SDF format, chain RA [auth D] SDF format, chain TA [auth D] SDF format, chain VA [auth D] SDF format, chain W [auth B] SDF format, chain WA [auth D] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] SDF format, chain ZA [auth D] SDF format, chain V [auth B] SDF format, chain F [auth A] SDF format, chain EB [auth D] MOL2 format, chain AA [auth B] MOL2 format, chain AB [auth D] MOL2 format, chain BB [auth D] MOL2 format, chain CA [auth B] MOL2 format, chain EA [auth C] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth C] MOL2 format, chain MA [auth C] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth C] MOL2 format, chain QA [auth C] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth D] MOL2 format, chain TA [auth D] MOL2 format, chain VA [auth D] MOL2 format, chain W [auth B] MOL2 format, chain WA [auth D] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain ZA [auth D] MOL2 format, chain V [auth B] MOL2 format, chain F [auth A] MOL2 format, chain EB [auth D] mmCIF format, chain AA [auth B] mmCIF format, chain AB [auth D] mmCIF format, chain BB [auth D] mmCIF format, chain CA [auth B] mmCIF format, chain EA [auth C] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth C] mmCIF format, chain HA [auth C] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth C] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth C] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth C] mmCIF format, chain MA [auth C] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth C] mmCIF format, chain QA [auth C] mmCIF format, chain R [auth A] mmCIF format, chain RA [auth D] mmCIF format, chain TA [auth D] mmCIF format, chain VA [auth D] mmCIF format, chain W [auth B] mmCIF format, chain WA [auth D] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain ZA [auth D] mmCIF format, chain V [auth B] mmCIF format, chain F [auth A] mmCIF format, chain EB [auth D]	AA [auth B] AB [auth D] BB [auth D] CA [auth B] EA [auth C] AA [auth B], AB [auth D], BB [auth D], CA [auth B], EA [auth C], EB [auth D], F [auth A], G [auth A], GA [auth C], HA [auth C], I [auth A], IA [auth C], J [auth A], K [auth A], KA [auth C], L [auth A], LA [auth C], MA [auth C], P [auth A], PA [auth C], QA [auth C], R [auth A], RA [auth D], TA [auth D], V [auth B], VA [auth D], W [auth B], WA [auth D], X [auth B], Y [auth B], Z [auth B], ZA [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain AB [auth D] Focus chain BB [auth D] Focus chain CA [auth B] Focus chain EA [auth C] Focus chain EB [auth D] Focus chain F [auth A] Focus chain G [auth A] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain I [auth A] Focus chain IA [auth C] Focus chain J [auth A] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain LA [auth C] Focus chain MA [auth C] Focus chain P [auth A] Focus chain PA [auth C] Focus chain QA [auth C] Focus chain R [auth A] Focus chain RA [auth D] Focus chain TA [auth D] Focus chain V [auth B] Focus chain VA [auth D] Focus chain W [auth B] Focus chain WA [auth D] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Focus chain ZA [auth D] Interactions & Density Focus chain AA [auth B] Focus chain AB [auth D] Focus chain BB [auth D] Focus chain CA [auth B] Focus chain EA [auth C] Focus chain EB [auth D] Focus chain F [auth A] Focus chain G [auth A] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain I [auth A] Focus chain IA [auth C] Focus chain J [auth A] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain LA [auth C] Focus chain MA [auth C] Focus chain P [auth A] Focus chain PA [auth C] Focus chain QA [auth C] Focus chain R [auth A] Focus chain RA [auth D] Focus chain TA [auth D] Focus chain V [auth B] Focus chain VA [auth D] Focus chain W [auth B] Focus chain WA [auth D] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Focus chain ZA [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.03 Å
R-Value Free: 0.243 (Depositor), 0.244 (DCC)
R-Value Work: 0.202 (Depositor), 0.206 (DCC)
R-Value Observed: 0.204 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.838	α = 90
b = 111.55	β = 90
c = 160.072	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
XDS	data reduction
XDS	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2015-01-21

Deposition Author(s):

Feil, S.C.

Parker, M.W.

Revision History (Full details and data files)

Version 1.0: 2015-01-21
Type: Initial release
Version 1.1: 2017-11-22
Changes: Refinement description
Version 1.2: 2024-02-28
Changes: Data collection, Database references, Derived calculations