6FT0

Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-425

PDB DOI: https://doi.org/10.2210/pdb6FT0/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: 2.10 Å
R-Value Free: 0.222
R-Value Work: 0.171
R-Value Observed: 0.173

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-425

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

To be published.

Macromolecule Content

Total Structure Weight: 174.15 kDa
Atom Count: 11,547
Modelled Residue Count: 1,301
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
E6E (Subject of Investigation/LOI) Query on E6E Download Ideal Coordinates CCD File SDF format, chain JB [auth D] SDF format, chain M [auth A] SDF format, chain NA [auth C] SDF format, chain Z [auth B] MOL2 format, chain JB [auth D] MOL2 format, chain M [auth A] MOL2 format, chain NA [auth C] MOL2 format, chain Z [auth B] mmCIF format, chain JB [auth D] mmCIF format, chain M [auth A] mmCIF format, chain NA [auth C] mmCIF format, chain Z [auth B]	JB [auth D], M [auth A], NA [auth C], Z [auth B]	4-{4-methoxy-3-[(2-methoxyphenyl)methoxy]phenyl}-2-(1-{thieno[3,2-d]pyrimidin-4-yl}piperidin-4-yl)-1,2,4a,5,8,8a-hexahydrophthalazin-1-one C₃₄ H₃₅ N₅ O₄ S FPUMGIJNOYNQAE-CLJLJLNGSA-N		Interactions Focus chain JB [auth D] Focus chain M [auth A] Focus chain NA [auth C] Focus chain Z [auth B] Interactions & Density Focus chain JB [auth D] Focus chain M [auth A] Focus chain NA [auth C] Focus chain Z [auth B]
EPE Query on EPE Download Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain LA [auth C] SDF format, chain MB [auth D] SDF format, chain N [auth A] SDF format, chain Y [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain LA [auth C] MOL2 format, chain MB [auth D] MOL2 format, chain N [auth A] MOL2 format, chain Y [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain LA [auth C] mmCIF format, chain MB [auth D] mmCIF format, chain N [auth A] mmCIF format, chain Y [auth B]	BA [auth B], LA [auth C], MB [auth D], N [auth A], Y [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain BA [auth B] Focus chain LA [auth C] Focus chain MB [auth D] Focus chain N [auth A] Focus chain Y [auth B] Interactions & Density Focus chain BA [auth B] Focus chain LA [auth C] Focus chain MB [auth D] Focus chain N [auth A] Focus chain Y [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain EB [auth D] SDF format, chain FB [auth D] SDF format, chain KB [auth D] MOL2 format, chain EB [auth D] MOL2 format, chain FB [auth D] MOL2 format, chain KB [auth D] mmCIF format, chain EB [auth D] mmCIF format, chain FB [auth D] mmCIF format, chain KB [auth D]	EB [auth D], FB [auth D], KB [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain EB [auth D] Focus chain FB [auth D] Focus chain KB [auth D] Interactions & Density Focus chain EB [auth D] Focus chain FB [auth D] Focus chain KB [auth D]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain FA [auth C] SDF format, chain R [auth B] SDF format, chain UA [auth D] MOL2 format, chain E [auth A] MOL2 format, chain FA [auth C] MOL2 format, chain R [auth B] MOL2 format, chain UA [auth D] mmCIF format, chain E [auth A] mmCIF format, chain FA [auth C] mmCIF format, chain R [auth B] mmCIF format, chain UA [auth D]	E [auth A], FA [auth C], R [auth B], UA [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain FA [auth C] Focus chain R [auth B] Focus chain UA [auth D] Interactions & Density Focus chain E [auth A] Focus chain FA [auth C] Focus chain R [auth B] Focus chain UA [auth D]
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 CB [auth D] SDF format, chain DA [auth B] SDF format, chain DB [auth D] SDF format, chain EA [auth C] SDF format, chain G [auth A] SDF format, chain GB [auth D] SDF format, chain H [auth A] SDF format, chain HA [auth C] SDF format, chain HB [auth D] SDF format, chain I [auth A] SDF format, chain IA [auth C] SDF format, chain IB [auth D] SDF format, chain J [auth A] SDF format, chain JA [auth C] SDF format, chain K [auth A] SDF format, chain KA [auth C] SDF format, chain L [auth A] SDF format, chain LB [auth D] SDF format, chain MA [auth C] SDF format, chain NB [auth D] SDF format, chain O [auth A] SDF format, chain OA [auth C] SDF format, chain P [auth A] SDF format, chain PA [auth C] SDF format, chain Q [auth A] SDF format, chain QA [auth C] SDF format, chain RA [auth C] SDF format, chain SA [auth C] SDF format, chain T [auth B] SDF format, chain TA [auth D] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain WA [auth D] SDF format, chain X [auth B] SDF format, chain XA [auth D] SDF format, chain YA [auth D] SDF format, chain ZA [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 CB [auth D] MOL2 format, chain DA [auth B] MOL2 format, chain DB [auth D] MOL2 format, chain EA [auth C] MOL2 format, chain G [auth A] MOL2 format, chain GB [auth D] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth C] MOL2 format, chain HB [auth D] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth C] MOL2 format, chain IB [auth D] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain LB [auth D] MOL2 format, chain MA [auth C] MOL2 format, chain NB [auth D] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth C] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth C] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth C] MOL2 format, chain RA [auth C] MOL2 format, chain SA [auth C] MOL2 format, chain T [auth B] MOL2 format, chain TA [auth D] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain WA [auth D] MOL2 format, chain X [auth B] MOL2 format, chain XA [auth D] MOL2 format, chain YA [auth D] MOL2 format, chain ZA [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 CB [auth D] mmCIF format, chain DA [auth B] mmCIF format, chain DB [auth D] mmCIF format, chain EA [auth C] mmCIF format, chain G [auth A] mmCIF format, chain GB [auth D] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth C] mmCIF format, chain HB [auth D] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth C] mmCIF format, chain IB [auth D] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth C] mmCIF format, chain L [auth A] mmCIF format, chain LB [auth D] mmCIF format, chain MA [auth C] mmCIF format, chain NB [auth D] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth C] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth C] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth C] mmCIF format, chain RA [auth C] mmCIF format, chain SA [auth C] mmCIF format, chain T [auth B] mmCIF format, chain TA [auth D] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain WA [auth D] mmCIF format, chain X [auth B] mmCIF format, chain XA [auth D] mmCIF format, chain YA [auth D] mmCIF format, chain ZA [auth D]	AA [auth B] AB [auth D] BB [auth D] CA [auth B] CB [auth D] AA [auth B], AB [auth D], BB [auth D], CA [auth B], CB [auth D], DA [auth B], DB [auth D], EA [auth C], G [auth A], GB [auth D], H [auth A], HA [auth C], HB [auth D], I [auth A], IA [auth C], IB [auth D], J [auth A], JA [auth C], K [auth A], KA [auth C], L [auth A], LB [auth D], MA [auth C], NB [auth D], O [auth A], OA [auth C], P [auth A], PA [auth C], Q [auth A], QA [auth C], RA [auth C], SA [auth C], T [auth B], TA [auth D], U [auth B], V [auth B], W [auth B], WA [auth D], X [auth B], XA [auth D], YA [auth D], 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 CB [auth D] Focus chain DA [auth B] Focus chain DB [auth D] Focus chain EA [auth C] Focus chain G [auth A] Focus chain GB [auth D] Focus chain H [auth A] Focus chain HA [auth C] Focus chain HB [auth D] Focus chain I [auth A] Focus chain IA [auth C] Focus chain IB [auth D] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain LB [auth D] Focus chain MA [auth C] Focus chain NB [auth D] Focus chain O [auth A] Focus chain OA [auth C] Focus chain P [auth A] Focus chain PA [auth C] Focus chain Q [auth A] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain SA [auth C] Focus chain T [auth B] Focus chain TA [auth D] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain WA [auth D] Focus chain X [auth B] Focus chain XA [auth D] Focus chain YA [auth D] 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 CB [auth D] Focus chain DA [auth B] Focus chain DB [auth D] Focus chain EA [auth C] Focus chain G [auth A] Focus chain GB [auth D] Focus chain H [auth A] Focus chain HA [auth C] Focus chain HB [auth D] Focus chain I [auth A] Focus chain IA [auth C] Focus chain IB [auth D] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain LB [auth D] Focus chain MA [auth C] Focus chain NB [auth D] Focus chain O [auth A] Focus chain OA [auth C] Focus chain P [auth A] Focus chain PA [auth C] Focus chain Q [auth A] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain SA [auth C] Focus chain T [auth B] Focus chain TA [auth D] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain WA [auth D] Focus chain X [auth B] Focus chain XA [auth D] Focus chain YA [auth D] Focus chain ZA [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain GA [auth C] SDF format, chain S [auth B] SDF format, chain VA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain GA [auth C] MOL2 format, chain S [auth B] MOL2 format, chain VA [auth D] mmCIF format, chain F [auth A] mmCIF format, chain GA [auth C] mmCIF format, chain S [auth B] mmCIF format, chain VA [auth D]	F [auth A], GA [auth C], S [auth B], VA [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain GA [auth C] Focus chain S [auth B] Focus chain VA [auth D] Interactions & Density Focus chain F [auth A] Focus chain GA [auth C] Focus chain S [auth B] Focus chain VA [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.222
R-Value Work: 0.171
R-Value Observed: 0.173
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.939	α = 90
b = 110.812	β = 90
c = 160.983	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
autoPROC	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