6FDI

Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-226


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 

Starting Model: experimental
View more details

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-226

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
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
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
D5T
Query on D5T

Download Ideal Coordinates CCD File 
FB [auth C],
OA [auth B],
R [auth A],
WB [auth D]
1-[2-[4-[(4~{a}~{S},8~{a}~{R})-4-(3,4-dimethoxyphenyl)-1-oxidanylidene-4~{a},5,8,8~{a}-tetrahydrophthalazin-2-yl]piperi din-1-yl]-2-oxidanylidene-ethyl]-4,4-dimethyl-piperidine-2,6-dione
C30 H38 N4 O6
DZMHUZHTZIODAZ-FCHUYYIVSA-N
EPE
Query on EPE

Download Ideal Coordinates CCD File 
EB [auth C],
MA [auth B]
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
PG4
Query on PG4

Download Ideal Coordinates CCD File 
CC [auth D]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
LA [auth B],
Q [auth A],
TB [auth D],
UB [auth D],
VB [auth D]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
DA [auth B],
E [auth A],
NB [auth D],
WA [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
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],
CA [auth A],
CB [auth C],
DB [auth C],
DC [auth D],
EC [auth D],
FA [auth B],
G [auth A],
GA [auth B],
GB [auth C],
H [auth A],
HA [auth B],
HB [auth C],
I [auth A],
IA [auth B],
IB [auth C],
J [auth A],
JA [auth B],
JB [auth C],
K [auth A],
KA [auth B],
KB [auth C],
L [auth A],
LB [auth D],
M [auth A],
MB [auth D],
N [auth A],
NA [auth B],
O [auth A],
P [auth A],
PA [auth B],
PB [auth D],
QA [auth B],
QB [auth D],
RA [auth B],
RB [auth D],
S [auth A],
SA [auth B],
SB [auth D],
T [auth A],
TA [auth C],
U [auth A],
UA [auth C],
V [auth A],
VA [auth C],
W [auth A],
X [auth A],
XB [auth D],
Y [auth A],
YA [auth C],
YB [auth D],
Z [auth A],
ZA [auth C],
ZB [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
EA [auth B],
F [auth A],
OB [auth D],
XA [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
D5T BindingDB:  6FDI Ki: 0.12 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.804α = 90
b = 111.042β = 90
c = 161.089γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-10
    Type: Initial release
  • Version 1.1: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary