4OGB

Crystal structure of the catalytic domain of PDE4D2 with compound 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

The PDE inhibition profile of LY294002 and tetrahydropyranyl analogues reveals a chromone motif for the development of PDE inhibitors

Howard, B.L.Nankervis, J.L.Feil, S.C.Manallack, D.T.Holien, J.K.Zhen, Z.Jennings, I.G.Abbott, B.M.Parker, M.W.Thompson, P.E.

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, D361Homo 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 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2SR
Query on 2SR

Download Ideal Coordinates CCD File 
E [auth A],
FA [auth C],
S [auth B],
SA [auth D]
(2R)-8-(3,4-dimethoxyphenyl)-6-methyl-2-(tetrahydro-2H-pyran-4-yl)-2H-chromen-4-ol
C23 H26 O5
RVKGQUJUMMUCKA-NRFANRHFSA-N
 Ligand Interaction
EPE
Query on EPE

Download Ideal Coordinates CCD File 
JA [auth C]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download Ideal Coordinates CCD File 
FB [auth D],
GB [auth D],
H [auth A],
XA [auth D]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

Download Ideal Coordinates CCD File 
BA [auth B],
DA [auth B],
O [auth A],
Q [auth A],
UA [auth D],
BA [auth B],
DA [auth B],
O [auth A],
Q [auth A],
UA [auth D],
YA [auth D]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
CB [auth D],
DB [auth D],
M [auth A],
N [auth A],
NA [auth C],
CB [auth D],
DB [auth D],
M [auth A],
N [auth A],
NA [auth C],
OA [auth C],
T [auth B],
U [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth B],
AB [auth D],
BB [auth D],
CA [auth B],
EA [auth C],
AA [auth B],
AB [auth D],
BB [auth D],
CA [auth B],
EA [auth C],
EB [auth D],
F [auth A],
G [auth A],
GA [auth C],
HA [auth C],
I [auth A],
IA [auth C],
J [auth A],
K [auth A],
KA [auth C],
L [auth A],
LA [auth C],
MA [auth C],
P [auth A],
PA [auth C],
QA [auth C],
R [auth A],
RA [auth D],
TA [auth D],
V [auth B],
VA [auth D],
W [auth B],
WA [auth D],
X [auth B],
Y [auth B],
Z [auth B],
ZA [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.838α = 90
b = 111.55β = 90
c = 160.072γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-01-21
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Refinement description