6FTA | pdb_00006fta

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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.34 Å
• R-Value Free: 
  0.240 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

hPDE4D2 structure with inhibitor NPD-3098

Singh, A.K., Brown, D.G.

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: 173.35 kDa 
• Atom Count: 11,415 
• Modeled Residue Count: 1,300 
• 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 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
E6N (Subject of Investigation/LOI)	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
EPE	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
PEG	TA [auth D], UA [auth D]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
ZN	BA [auth C], E [auth A], JA [auth D], P [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	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
MG	CA [auth C], F [auth A], KA [auth D], Q [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.34 Å
• R-Value Free:  0.240 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

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

Entry History 

Deposition Data

• Released Date: 2019-03-20 
Deposition Author(s): Singh, A.K., Brown, D.G.

Revision History  

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