6FET | pdb_00006fet

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 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.171 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 
    0.173 (Depositor) 

wwPDB Validation 3D Report Full Report

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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-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.

Macromolecule Content 

  • Total Structure Weight: 176.36 kDa 
  • Atom Count: 11,731 
  • Modeled Residue Count: 1,300 
  • Deposited Residue Count: 1,456 
  • Unique protein chains: 1

Macromolecules

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|  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: 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 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ08499
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 8 Unique
IDChains Name / 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
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
PG4

Query on PG4


Download:Ideal Coordinates CCD File
MB [auth C],
SB [auth D]		TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
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
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
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
NI

Query on NI


Download:Ideal Coordinates CCD File
CA [auth A],
RC [auth D]		NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
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
Binding Affinity Annotations 
IDSourceBinding Affinity
D68 BindingDB:  6FET Ki: 0.3 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free:  0.199 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.171 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 0.173 (Depositor) 
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

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-24
    Type: Initial release
  • Version 1.1: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Refinement description