6FDI

Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-226

PDB DOI: https://doi.org/10.2210/pdb6FDI/pdb

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

Deposited: 2017-12-24 Released: 2019-04-10
Deposition Author(s): Singh, A.K., Brown, D.G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.200
R-Value Work: 0.174
R-Value Observed: 0.175

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-226

Salado, I.G., Moreno, C., Sakaine, G., Singh, A.K., Blaazer, A.R., Siderius, M., Matheeussen, A., Gul, S., Maes, L., Leurs, R., Brown, D.G., Augustyns, K.

To be published.

Macromolecule Content

Total Structure Weight: 174.66 kDa
Atom Count: 11,886
Modelled Residue Count: 1,303
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 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
D5T Query on D5T Download Ideal Coordinates CCD File SDF format, chain WB [auth D] SDF format, chain FB [auth C] SDF format, chain OA [auth B] SDF format, chain R [auth A] MOL2 format, chain WB [auth D] MOL2 format, chain FB [auth C] MOL2 format, chain OA [auth B] MOL2 format, chain R [auth A] mmCIF format, chain WB [auth D] mmCIF format, chain FB [auth C] mmCIF format, chain OA [auth B] mmCIF format, chain R [auth A]	FB [auth C], OA [auth B], R [auth A], WB [auth D]	1-[2-[4-[(4~{a}~{S},8~{a}~{R})-4-(3,4-dimethoxyphenyl)-1-oxidanylidene-4~{a},5,8,8~{a}-tetrahydrophthalazin-2-yl]piperi din-1-yl]-2-oxidanylidene-ethyl]-4,4-dimethyl-piperidine-2,6-dione C₃₀ H₃₈ N₄ O₆ DZMHUZHTZIODAZ-FCHUYYIVSA-N		Interactions Focus chain FB [auth C] Focus chain OA [auth B] Focus chain R [auth A] Focus chain WB [auth D] Interactions & Density Focus chain FB [auth C] Focus chain OA [auth B] Focus chain R [auth A] Focus chain WB [auth D]
EPE Query on EPE Download Ideal Coordinates CCD File SDF format, chain EB [auth C] SDF format, chain MA [auth B] MOL2 format, chain EB [auth C] MOL2 format, chain MA [auth B] mmCIF format, chain EB [auth C] mmCIF format, chain MA [auth B]	EB [auth C], MA [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain EB [auth C] Focus chain MA [auth B] Interactions & Density Focus chain EB [auth C] Focus chain MA [auth B]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain CC [auth D] MOL2 format, chain CC [auth D] mmCIF format, chain CC [auth D]	CC [auth D]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain CC [auth D] Interactions & Density Focus chain CC [auth D]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain LA [auth B] SDF format, chain Q [auth A] SDF format, chain VB [auth D] SDF format, chain TB [auth D] SDF format, chain UB [auth D] MOL2 format, chain LA [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain VB [auth D] MOL2 format, chain TB [auth D] MOL2 format, chain UB [auth D] mmCIF format, chain LA [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain VB [auth D] mmCIF format, chain TB [auth D] mmCIF format, chain UB [auth D]	LA [auth B], Q [auth A], TB [auth D], UB [auth D], VB [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain LA [auth B] Focus chain Q [auth A] Focus chain TB [auth D] Focus chain UB [auth D] Focus chain VB [auth D] Interactions & Density Focus chain LA [auth B] Focus chain Q [auth A] Focus chain TB [auth D] Focus chain UB [auth D] Focus chain VB [auth D]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain WA [auth C] SDF format, chain DA [auth B] SDF format, chain E [auth A] SDF format, chain NB [auth D] MOL2 format, chain WA [auth C] MOL2 format, chain DA [auth B] MOL2 format, chain E [auth A] MOL2 format, chain NB [auth D] mmCIF format, chain WA [auth C] mmCIF format, chain DA [auth B] mmCIF format, chain E [auth A] mmCIF format, chain NB [auth D]	DA [auth B], E [auth A], NB [auth D], WA [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain DA [auth B] Focus chain E [auth A] Focus chain NB [auth D] Focus chain WA [auth C] Interactions & Density Focus chain DA [auth B] Focus chain E [auth A] Focus chain NB [auth D] Focus chain WA [auth C]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain BC [auth D] SDF format, chain EC [auth D] SDF format, chain FA [auth B] SDF format, chain GB [auth C] SDF format, chain HB [auth C] SDF format, chain IB [auth C] SDF format, chain J [auth A] SDF format, chain KA [auth B] SDF format, chain L [auth A] SDF format, chain NA [auth B] SDF format, chain PB [auth D] SDF format, chain SB [auth D] SDF format, chain T [auth A] SDF format, chain TA [auth C] SDF format, chain UA [auth C] SDF format, chain V [auth A] SDF format, chain VA [auth C] SDF format, chain W [auth A] SDF format, chain X [auth A] SDF format, chain YA [auth C] SDF format, chain ZA [auth C] SDF format, chain ZB [auth D] SDF format, chain AA [auth A] SDF format, chain AB [auth C] SDF format, chain AC [auth D] SDF format, chain BA [auth A] SDF format, chain BB [auth C] SDF format, chain CA [auth A] SDF format, chain CB [auth C] SDF format, chain DB [auth C] SDF format, chain DC [auth D] SDF format, chain G [auth A] SDF format, chain GA [auth B] SDF format, chain H [auth A] SDF format, chain HA [auth B] SDF format, chain I [auth A] SDF format, chain IA [auth B] SDF format, chain JA [auth B] SDF format, chain JB [auth C] SDF format, chain K [auth A] SDF format, chain KB [auth C] SDF format, chain LB [auth D] SDF format, chain M [auth A] SDF format, chain MB [auth D] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain PA [auth B] SDF format, chain QA [auth B] SDF format, chain QB [auth D] SDF format, chain RA [auth B] SDF format, chain RB [auth D] SDF format, chain S [auth A] SDF format, chain SA [auth B] SDF format, chain U [auth A] SDF format, chain XB [auth D] SDF format, chain Y [auth A] SDF format, chain YB [auth D] SDF format, chain Z [auth A] MOL2 format, chain BC [auth D] MOL2 format, chain EC [auth D] MOL2 format, chain FA [auth B] MOL2 format, chain GB [auth C] MOL2 format, chain HB [auth C] MOL2 format, chain IB [auth C] MOL2 format, chain J [auth A] MOL2 format, chain KA [auth B] MOL2 format, chain L [auth A] MOL2 format, chain NA [auth B] MOL2 format, chain PB [auth D] MOL2 format, chain SB [auth D] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth C] MOL2 format, chain UA [auth C] MOL2 format, chain V [auth A] MOL2 format, chain VA [auth C] MOL2 format, chain W [auth A] MOL2 format, chain X [auth A] MOL2 format, chain YA [auth C] MOL2 format, chain ZA [auth C] MOL2 format, chain ZB [auth D] MOL2 format, chain AA [auth A] MOL2 format, chain AB [auth C] MOL2 format, chain AC [auth D] MOL2 format, chain BA [auth A] MOL2 format, chain BB [auth C] MOL2 format, chain CA [auth A] MOL2 format, chain CB [auth C] MOL2 format, chain DB [auth C] MOL2 format, chain DC [auth D] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth B] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth B] MOL2 format, chain JA [auth B] MOL2 format, chain JB [auth C] MOL2 format, chain K [auth A] MOL2 format, chain KB [auth C] MOL2 format, chain LB [auth D] MOL2 format, chain M [auth A] MOL2 format, chain MB [auth D] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth B] MOL2 format, chain QA [auth B] MOL2 format, chain QB [auth D] MOL2 format, chain RA [auth B] MOL2 format, chain RB [auth D] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth B] MOL2 format, chain U [auth A] MOL2 format, chain XB [auth D] MOL2 format, chain Y [auth A] MOL2 format, chain YB [auth D] MOL2 format, chain Z [auth A] mmCIF format, chain BC [auth D] mmCIF format, chain EC [auth D] mmCIF format, chain FA [auth B] mmCIF format, chain GB [auth C] mmCIF format, chain HB [auth C] mmCIF format, chain IB [auth C] mmCIF format, chain J [auth A] mmCIF format, chain KA [auth B] mmCIF format, chain L [auth A] mmCIF format, chain NA [auth B] mmCIF format, chain PB [auth D] mmCIF format, chain SB [auth D] mmCIF format, chain T [auth A] mmCIF format, chain TA [auth C] mmCIF format, chain UA [auth C] mmCIF format, chain V [auth A] mmCIF format, chain VA [auth C] mmCIF format, chain W [auth A] mmCIF format, chain X [auth A] mmCIF format, chain YA [auth C] mmCIF format, chain ZA [auth C] mmCIF format, chain ZB [auth D] mmCIF format, chain AA [auth A] mmCIF format, chain AB [auth C] mmCIF format, chain AC [auth D] mmCIF format, chain BA [auth A] mmCIF format, chain BB [auth C] mmCIF format, chain CA [auth A] mmCIF format, chain CB [auth C] mmCIF format, chain DB [auth C] mmCIF format, chain DC [auth D] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth B] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth B] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth B] mmCIF format, chain JA [auth B] mmCIF format, chain JB [auth C] mmCIF format, chain K [auth A] mmCIF format, chain KB [auth C] mmCIF format, chain LB [auth D] mmCIF format, chain M [auth A] mmCIF format, chain MB [auth D] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth B] mmCIF format, chain QA [auth B] mmCIF format, chain QB [auth D] mmCIF format, chain RA [auth B] mmCIF format, chain RB [auth D] mmCIF format, chain S [auth A] mmCIF format, chain SA [auth B] mmCIF format, chain U [auth A] mmCIF format, chain XB [auth D] mmCIF format, chain Y [auth A] mmCIF format, chain YB [auth D] mmCIF format, chain Z [auth A]	AA [auth A] AB [auth C] AC [auth D] BA [auth A] BB [auth C] AA [auth A], AB [auth C], AC [auth D], BA [auth A], BB [auth C], BC [auth D], CA [auth A], CB [auth C], DB [auth C], DC [auth D], EC [auth D], FA [auth B], G [auth A], GA [auth B], GB [auth C], H [auth A], HA [auth B], HB [auth C], I [auth A], IA [auth B], IB [auth C], J [auth A], JA [auth B], JB [auth C], K [auth A], KA [auth B], KB [auth C], L [auth A], LB [auth D], M [auth A], MB [auth D], N [auth A], NA [auth B], O [auth A], P [auth A], PA [auth B], PB [auth D], QA [auth B], QB [auth D], RA [auth B], RB [auth D], S [auth A], SA [auth B], SB [auth D], T [auth A], TA [auth C], U [auth A], UA [auth C], V [auth A], VA [auth C], W [auth A], X [auth A], XB [auth D], Y [auth A], YA [auth C], YB [auth D], Z [auth A], ZA [auth C], ZB [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain AB [auth C] Focus chain AC [auth D] Focus chain BA [auth A] Focus chain BB [auth C] Focus chain BC [auth D] Focus chain CA [auth A] Focus chain CB [auth C] Focus chain DB [auth C] Focus chain DC [auth D] Focus chain EC [auth D] Focus chain FA [auth B] Focus chain G [auth A] Focus chain GA [auth B] Focus chain GB [auth C] Focus chain H [auth A] Focus chain HA [auth B] Focus chain HB [auth C] Focus chain I [auth A] Focus chain IA [auth B] Focus chain IB [auth C] Focus chain J [auth A] Focus chain JA [auth B] Focus chain JB [auth C] Focus chain K [auth A] Focus chain KA [auth B] Focus chain KB [auth C] Focus chain L [auth A] Focus chain LB [auth D] Focus chain M [auth A] Focus chain MB [auth D] Focus chain N [auth A] Focus chain NA [auth B] Focus chain O [auth A] Focus chain P [auth A] Focus chain PA [auth B] Focus chain PB [auth D] Focus chain QA [auth B] Focus chain QB [auth D] Focus chain RA [auth B] Focus chain RB [auth D] Focus chain S [auth A] Focus chain SA [auth B] Focus chain SB [auth D] Focus chain T [auth A] Focus chain TA [auth C] Focus chain U [auth A] Focus chain UA [auth C] Focus chain V [auth A] Focus chain VA [auth C] Focus chain W [auth A] Focus chain X [auth A] Focus chain XB [auth D] Focus chain Y [auth A] Focus chain YA [auth C] Focus chain YB [auth D] Focus chain Z [auth A] Focus chain ZA [auth C] Focus chain ZB [auth D] Interactions & Density Focus chain AA [auth A] Focus chain AB [auth C] Focus chain AC [auth D] Focus chain BA [auth A] Focus chain BB [auth C] Focus chain BC [auth D] Focus chain CA [auth A] Focus chain CB [auth C] Focus chain DB [auth C] Focus chain DC [auth D] Focus chain EC [auth D] Focus chain FA [auth B] Focus chain G [auth A] Focus chain GA [auth B] Focus chain GB [auth C] Focus chain H [auth A] Focus chain HA [auth B] Focus chain HB [auth C] Focus chain I [auth A] Focus chain IA [auth B] Focus chain IB [auth C] Focus chain J [auth A] Focus chain JA [auth B] Focus chain JB [auth C] Focus chain K [auth A] Focus chain KA [auth B] Focus chain KB [auth C] Focus chain L [auth A] Focus chain LB [auth D] Focus chain M [auth A] Focus chain MB [auth D] Focus chain N [auth A] Focus chain NA [auth B] Focus chain O [auth A] Focus chain P [auth A] Focus chain PA [auth B] Focus chain PB [auth D] Focus chain QA [auth B] Focus chain QB [auth D] Focus chain RA [auth B] Focus chain RB [auth D] Focus chain S [auth A] Focus chain SA [auth B] Focus chain SB [auth D] Focus chain T [auth A] Focus chain TA [auth C] Focus chain U [auth A] Focus chain UA [auth C] Focus chain V [auth A] Focus chain VA [auth C] Focus chain W [auth A] Focus chain X [auth A] Focus chain XB [auth D] Focus chain Y [auth A] Focus chain YA [auth C] Focus chain YB [auth D] Focus chain Z [auth A] Focus chain ZA [auth C] Focus chain ZB [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain XA [auth C] SDF format, chain EA [auth B] SDF format, chain F [auth A] SDF format, chain OB [auth D] MOL2 format, chain XA [auth C] MOL2 format, chain EA [auth B] MOL2 format, chain F [auth A] MOL2 format, chain OB [auth D] mmCIF format, chain XA [auth C] mmCIF format, chain EA [auth B] mmCIF format, chain F [auth A] mmCIF format, chain OB [auth D]	EA [auth B], F [auth A], OB [auth D], XA [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain EA [auth B] Focus chain F [auth A] Focus chain OB [auth D] Focus chain XA [auth C] Interactions & Density Focus chain EA [auth B] Focus chain F [auth A] Focus chain OB [auth D] Focus chain XA [auth C]

Binding Affinity Annotations
ID	Source	Binding Affinity
D5T	BindingDB: 6FDI	Ki: 0.12 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.200
R-Value Work: 0.174
R-Value Observed: 0.175
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.804	α = 90
b = 111.042	β = 90
c = 161.089	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: 2019-04-10

Deposition Author(s):

Singh, A.K.

Brown, D.G.

Revision History (Full details and data files)

Version 1.0: 2019-04-10
Type: Initial release
Version 1.1: 2024-01-17
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary