6FE7 | pdb_00006fe7

Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-356

• PDB DOI: https://doi.org/10.2210/pdb6FE7/pdb

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


• Deposited: 2017-12-29 Released: 2019-04-10 
• Deposition Author(s): Singh, A.K., Brown, D.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.200 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Literature

hPDE4D2 structure with inhibitor NPD-356

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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 176.33 kDa 
• Atom Count: 11,789 
• Modeled Residue Count: 1,301 
• Deposited Residue Count: 1,456 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
D62	KC [auth D], RB [auth C], SA [auth B], X [auth A]	(4aS,8aR)-2-(1-{2-aminothieno[2,3-d]pyrimidin-4-yl}piperidin-4-yl)-4-(3,4- dimethoxyphenyl)-1,2,4a,5,8,8a-hexahydrophthalazin-1-one C27 H30 N6 O3 S VRSCGUCAJHMOSB-RBUKOAKNSA-N
EPE	BA [auth A], LA [auth B], LB [auth C], QC [auth D], XA [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
PG4	SB [auth C], ZA [auth C]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PEG	BC [auth D], CC [auth D], DC [auth D], KA [auth B], KB [auth C], LC [auth D], MC [auth D], N [auth A], O [auth A], QB [auth C], T [auth A], U [auth A], V [auth A], W [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
ZN	CB [auth C], DA [auth B], E [auth A], VB [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	AA [auth A], AB [auth C], AC [auth D], BB [auth C], CA [auth A], EB [auth C], EC [auth D], FA [auth B], FB [auth C], FC [auth D], G [auth A], GA [auth B], GB [auth C], GC [auth D], H [auth A], HA [auth B], HB [auth C], HC [auth D], I [auth A], IA [auth B], IB [auth C], IC [auth D], J [auth A], JA [auth B], JB [auth C], JC [auth D], K [auth A], L [auth A], M [auth A], MA [auth B], MB [auth C], NA [auth B], NB [auth C], NC [auth D], OA [auth B], OB [auth C], OC [auth D], P [auth A], PA [auth B], PB [auth C], PC [auth D], Q [auth A], QA [auth B], R [auth A], RA [auth B], S [auth A], TA [auth B], TB [auth C], UA [auth B], UB [auth D], VA [auth B], WA [auth B], XB [auth D], Y [auth A], YA [auth C], YB [auth D], Z [auth A], ZB [auth D]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG	DB [auth C], EA [auth B], F [auth A], WB [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
D62	BindingDB:  6FE7	Ki: 0.35 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.200 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.22	α = 90
b = 111.03	β = 90
c = 160.96	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-04-10 
Deposition Author(s): Singh, A.K., Brown, D.G.

Revision History  

• Version 1.0: 2019-04-10
  Type: Initial release
  
• Version 1.1: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Refinement description