6FTA

Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-3098

PDB DOI: https://doi.org/10.2210/pdb6FTA/pdb

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

Deposited: 2018-02-20 Released: 2019-03-20
Deposition Author(s): Singh, A.K., Brown, D.G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.34 Å
R-Value Free: 0.240
R-Value Work: 0.181
R-Value Observed: 0.184

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

hPDE4D2 structure with inhibitor NPD-3098

Singh, A.K., Brown, D.G.

To be published.

Macromolecule Content

Total Structure Weight: 173.35 kDa
Atom Count: 11,415
Modelled Residue Count: 1,300
Deposited Residue Count: 1,456
Unique protein chains: 1

Macromolecules

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(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	364	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% 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
E6N (Subject of Investigation/LOI) Query on E6N Download Ideal Coordinates CCD File SDF format, chain GA [auth C] SDF format, chain N [auth A] SDF format, chain VA [auth D] SDF format, chain W [auth B] MOL2 format, chain GA [auth C] MOL2 format, chain N [auth A] MOL2 format, chain VA [auth D] MOL2 format, chain W [auth B] mmCIF format, chain GA [auth C] mmCIF format, chain N [auth A] mmCIF format, chain VA [auth D] mmCIF format, chain W [auth B]	GA [auth C], N [auth A], VA [auth D], W [auth B]	(4~{a}~{S},8~{a}~{S})-4-[4-methoxy-3-[(2-methoxyphenyl)methoxy]phenyl]-2-[1-(3-nitroimidazo[1,2-b]pyridazin-6-yl)piperidin-4-yl]-4~{a},5,6,7,8,8~{a}-hexahydrophthalazin-1-one C₃₄ H₃₇ N₇ O₆ ZKCRNRMMYMOGBM-UIOOFZCWSA-N		Interactions Focus chain GA [auth C] Focus chain N [auth A] Focus chain VA [auth D] Focus chain W [auth B] Interactions & Density Focus chain GA [auth C] Focus chain N [auth A] Focus chain VA [auth D] Focus chain W [auth B]
EPE Query on EPE Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain FA [auth C] SDF format, chain O [auth A] SDF format, chain Z [auth B] SDF format, chain ZA [auth D] MOL2 format, chain AA [auth B] MOL2 format, chain FA [auth C] MOL2 format, chain O [auth A] MOL2 format, chain Z [auth B] MOL2 format, chain ZA [auth D] mmCIF format, chain AA [auth B] mmCIF format, chain FA [auth C] mmCIF format, chain O [auth A] mmCIF format, chain Z [auth B] mmCIF format, chain ZA [auth D]	AA [auth B], FA [auth C], O [auth A], Z [auth B], ZA [auth D]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain FA [auth C] Focus chain O [auth A] Focus chain Z [auth B] Focus chain ZA [auth D] Interactions & Density Focus chain AA [auth B] Focus chain FA [auth C] Focus chain O [auth A] Focus chain Z [auth B] Focus chain ZA [auth D]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain TA [auth D] SDF format, chain UA [auth D] MOL2 format, chain TA [auth D] MOL2 format, chain UA [auth D] mmCIF format, chain TA [auth D] mmCIF format, chain UA [auth D]	TA [auth D], UA [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain TA [auth D] Focus chain UA [auth D] Interactions & Density Focus chain TA [auth D] Focus chain UA [auth D]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain E [auth A] SDF format, chain JA [auth D] SDF format, chain P [auth B] MOL2 format, chain BA [auth C] MOL2 format, chain E [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain P [auth B] mmCIF format, chain BA [auth C] mmCIF format, chain E [auth A] mmCIF format, chain JA [auth D] mmCIF format, chain P [auth B]	BA [auth C], E [auth A], JA [auth D], P [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Focus chain E [auth A] Focus chain JA [auth D] Focus chain P [auth B] Interactions & Density Focus chain BA [auth C] Focus chain E [auth A] Focus chain JA [auth D] Focus chain P [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain DA [auth C] SDF format, chain EA [auth C] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain HA [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 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 OA [auth D] SDF format, chain PA [auth D] SDF format, chain QA [auth D] SDF format, chain R [auth B] 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 U [auth B] SDF format, chain V [auth B] SDF format, chain WA [auth D] SDF format, chain X [auth B] SDF format, chain XA [auth D] SDF format, chain Y [auth B] SDF format, chain YA [auth D] MOL2 format, chain DA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain HA [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 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 OA [auth D] MOL2 format, chain PA [auth D] MOL2 format, chain QA [auth D] MOL2 format, chain R [auth B] 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 U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain WA [auth D] MOL2 format, chain X [auth B] MOL2 format, chain XA [auth D] MOL2 format, chain Y [auth B] MOL2 format, chain YA [auth D] mmCIF format, chain DA [auth C] mmCIF format, chain EA [auth C] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth C] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] 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 OA [auth D] mmCIF format, chain PA [auth D] mmCIF format, chain QA [auth D] mmCIF format, chain R [auth B] mmCIF format, chain RA [auth D] mmCIF format, chain S [auth B] mmCIF format, chain SA [auth D] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain WA [auth D] mmCIF format, chain X [auth B] mmCIF format, chain XA [auth D] mmCIF format, chain Y [auth B] mmCIF format, chain YA [auth D]	DA [auth C] EA [auth C] G [auth A] H [auth A] HA [auth C] DA [auth C], EA [auth C], G [auth A], H [auth A], HA [auth C], 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], OA [auth D], PA [auth D], QA [auth D], R [auth B], RA [auth D], S [auth B], SA [auth D], T [auth B], U [auth B], V [auth B], WA [auth D], X [auth B], XA [auth D], Y [auth B], YA [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain DA [auth C] Focus chain EA [auth C] Focus chain G [auth A] Focus chain H [auth A] Focus chain HA [auth C] 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 OA [auth D] Focus chain PA [auth D] Focus chain QA [auth D] Focus chain R [auth B] Focus chain RA [auth D] Focus chain S [auth B] Focus chain SA [auth D] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain WA [auth D] Focus chain X [auth B] Focus chain XA [auth D] Focus chain Y [auth B] Focus chain YA [auth D] Interactions & Density Focus chain DA [auth C] Focus chain EA [auth C] Focus chain G [auth A] Focus chain H [auth A] Focus chain HA [auth C] 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 OA [auth D] Focus chain PA [auth D] Focus chain QA [auth D] Focus chain R [auth B] Focus chain RA [auth D] Focus chain S [auth B] Focus chain SA [auth D] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain WA [auth D] Focus chain X [auth B] Focus chain XA [auth D] Focus chain Y [auth B] Focus chain YA [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain F [auth A] SDF format, chain KA [auth D] SDF format, chain Q [auth B] MOL2 format, chain CA [auth C] MOL2 format, chain F [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain Q [auth B] mmCIF format, chain CA [auth C] mmCIF format, chain F [auth A] mmCIF format, chain KA [auth D] mmCIF format, chain Q [auth B]	CA [auth C], F [auth A], KA [auth D], Q [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain CA [auth C] Focus chain F [auth A] Focus chain KA [auth D] Focus chain Q [auth B] Interactions & Density Focus chain CA [auth C] Focus chain F [auth A] Focus chain KA [auth D] Focus chain Q [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.34 Å
R-Value Free: 0.240
R-Value Work: 0.181
R-Value Observed: 0.184
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.99	α = 90
b = 110.76	β = 90
c = 161.34	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2019-03-20

Deposition Author(s):

Singh, A.K.

Brown, D.G.

Revision History (Full details and data files)

Version 1.0: 2019-03-20
Type: Initial release
Version 1.1: 2024-01-17
Changes: Data collection, Database references, Derived calculations, Refinement description