7AB9

Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-656


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 

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-656

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

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
cAMP-specific 3',5'-cyclic phosphodiesterase 4D
A, B, C, D
364Homo sapiensMutation(s): 0 
Gene Names: PDE4DDPDE3
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ08499
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QWZ (Subject of Investigation/LOI)
Query on QWZ

Download Ideal Coordinates CCD File 
HA [auth C],
P [auth A],
WA [auth D],
Y [auth B]
1-cycloheptyl-3-{4-methoxy-3-[2-(4-methoxyphenyl)ethoxy]phenyl}-4,4-dimethyl-4,5-dihydro-1H-pyrazol-5-one
C28 H36 N2 O4
RIACCCXIOWXEOM-UHFFFAOYSA-N
EPE
Query on EPE

Download Ideal Coordinates CCD File 
GA [auth C],
UA [auth D]
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A],
IA [auth D],
R [auth B],
Z [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
BA [auth C]
CA [auth C]
DA [auth C]
EA [auth C]
FA [auth C]
BA [auth C],
CA [auth C],
DA [auth C],
EA [auth C],
FA [auth C],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
KA [auth D],
L [auth A],
LA [auth D],
M [auth A],
MA [auth D],
N [auth A],
NA [auth D],
O [auth A],
OA [auth D],
PA [auth D],
Q [auth A],
QA [auth D],
RA [auth D],
SA [auth D],
T [auth B],
TA [auth D],
U [auth B],
V [auth B],
VA [auth D],
W [auth B],
X [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG
Query on MG

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AA [auth C],
F [auth A],
JA [auth D],
S [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.168α = 90
b = 111.797β = 90
c = 160.261γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Union (EU)European Union602666

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-06
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description