6FT0 | pdb_00006ft0

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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.222 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Starting Model: experimental

Literature

hPDE4D2 structure with inhibitor NPD-425

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: 174.15 kDa 
• Atom Count: 11,547 
• 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 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
E6E (Subject of Investigation/LOI)	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
EPE	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
PEG	EB [auth D], FB [auth D], KB [auth D]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
ZN	E [auth A], FA [auth C], R [auth B], UA [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	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
MG	F [auth A], GA [auth C], S [auth B], VA [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.222 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

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

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