7A8Q

Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-654


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

hPDE4D2 structure with inhibitor NPD-654

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 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
R4H (Subject of Investigation/LOI)
Query on R4H

Download Ideal Coordinates CCD File 
GA [auth C],
UA [auth D],
X [auth B]
2-cycloheptyl-5-[4-methoxy-3-[[4-(1~{H}-1,2,3,4-tetrazol-5-yl)phenyl]methoxy]phenyl]-4,4-dimethyl-pyrazolidin-3-one
C27 H34 N6 O3
QTPLHRMVDWVYKA-XMMPIXPASA-N
EPE
Query on EPE

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FA [auth C],
N [auth A],
Y [auth B],
YA [auth D],
Z [auth B]
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
PEG
Query on PEG

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HA [auth C],
VA [auth D],
WA [auth D],
XA [auth D]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
ZN
Query on ZN

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AA [auth C],
E [auth A],
JA [auth D],
Q [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO
Query on EDO

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CA [auth C]
DA [auth C]
EA [auth C]
G [auth A]
H [auth A]
CA [auth C],
DA [auth C],
EA [auth C],
G [auth A],
H [auth A],
I [auth A],
IA [auth C],
J [auth A],
K [auth A],
L [auth A],
LA [auth D],
M [auth A],
MA [auth D],
NA [auth D],
O [auth A],
OA [auth D],
P [auth A],
PA [auth D],
QA [auth D],
RA [auth D],
S [auth B],
SA [auth D],
T [auth B],
TA [auth D],
U [auth B],
V [auth B],
W [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG
Query on MG

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BA [auth C],
F [auth A],
KA [auth D],
R [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.349α = 90
b = 111.441β = 90
c = 160.227γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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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