6FET

Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-1439


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

hPDE4D2 structure with inhibitor NPD-1439

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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
cAMP-specific 3',5'-cyclic phosphodiesterase 4DA, B, C, D364Homo 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ08499
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
D68 (Subject of Investigation/LOI)
Query on D68

Download Ideal Coordinates CCD File 
KC [auth D],
NB [auth C],
QA [auth B],
U [auth A]
1-(2-{4-[(4aS,8aR)-4-[3,4-bis(difluoromethoxy)phenyl]-1-oxo-1,2,4a,5,8,8a-hexahydrophthalazin-2-yl]piperidin-1-yl}-2-oxoethyl)-4,4-dimethylpiperidine-2,6-dione
C30 H34 F4 N4 O6
WVAQTVIALKSAMT-VQTJNVASSA-N
 Ligand Interaction
EPE
Query on EPE

Download Ideal Coordinates CCD File 
JA [auth B],
KB [auth C],
LC [auth D],
PA [auth B],
V [auth A]
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
PG4
Query on PG4

Download Ideal Coordinates CCD File 
MB [auth C],
SB [auth D]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download Ideal Coordinates CCD File 
JB [auth C],
JC [auth D],
N [auth A],
OA [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
CB [auth C],
DA [auth B],
E [auth A],
UB [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth A],
AB [auth C],
AC [auth D],
BA [auth A],
BB [auth C],
AA [auth A],
AB [auth C],
AC [auth D],
BA [auth A],
BB [auth C],
BC [auth D],
CC [auth D],
DC [auth D],
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],
K [auth A],
KA [auth B],
L [auth A],
LA [auth B],
LB [auth C],
M [auth A],
MA [auth B],
MC [auth D],
NA [auth B],
NC [auth D],
O [auth A],
OB [auth C],
OC [auth D],
P [auth A],
PB [auth C],
PC [auth D],
Q [auth A],
QB [auth C],
QC [auth D],
R [auth A],
RA [auth B],
RB [auth D],
S [auth A],
SA [auth B],
T [auth A],
TA [auth B],
TB [auth D],
UA [auth B],
VA [auth B],
W [auth A],
WA [auth B],
WB [auth D],
X [auth A],
XA [auth B],
XB [auth D],
Y [auth A],
YA [auth B],
YB [auth D],
Z [auth A],
ZA [auth C],
ZB [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

Download Ideal Coordinates CCD File 
CA [auth A],
RC [auth D]
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
DB [auth C],
EA [auth B],
F [auth A],
VB [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.19α = 90
b = 110.71β = 90
c = 161.48γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-24
    Type: Initial release