7AAG

Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-617


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.168 

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-617

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
Expand
  • Reference Sequence
Small Molecules
Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QWT (Subject of Investigation/LOI)
Query on QWT

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BB [auth C],
G [auth A],
HA [auth B],
TB [auth D]
1-cycloheptyl-3-(4-methoxy-3-{4-[4-(1H-1,2,3,4-tetrazol-5-yl)phenoxy]butoxy}phenyl)-4,4-dimethyl-4,5-dihydro-1H-pyrazol-5-one
C30 H38 N6 O4
JPXAIORZGBCHIB-UHFFFAOYSA-N
EPE
Query on EPE

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JB [auth C],
KC [auth D],
SA [auth B],
TA [auth B],
W [auth A]
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
ILE
Query on ILE

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XA [auth C]ISOLEUCINE
C6 H13 N O2
AGPKZVBTJJNPAG-WHFBIAKZSA-N
PRO
Query on PRO

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YA [auth C]PROLINE
C5 H9 N O2
ONIBWKKTOPOVIA-BYPYZUCNSA-N
PEG
Query on PEG

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FC [auth D],
GC [auth D],
HB [auth C],
P [auth A],
PB [auth D]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
DMS
Query on DMS

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HC [auth D]
IB [auth C]
IC [auth D]
Q [auth A]
QA [auth B]
HC [auth D],
IB [auth C],
IC [auth D],
Q [auth A],
QA [auth B],
R [auth A],
RA [auth B],
S [auth A],
T [auth A],
U [auth A],
VA [auth B],
WA [auth C]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN
Query on ZN

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E [auth A],
FA [auth B],
RB [auth D],
ZA [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO
Query on EDO

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AA [auth A]
AC [auth D]
BA [auth A]
BC [auth D]
CB [auth C]
AA [auth A],
AC [auth D],
BA [auth A],
BC [auth D],
CB [auth C],
CC [auth D],
DA [auth A],
DB [auth C],
DC [auth D],
EA [auth B],
EB [auth C],
EC [auth D],
FB [auth C],
GB [auth C],
H [auth A],
I [auth A],
IA [auth B],
J [auth A],
JA [auth B],
JC [auth D],
K [auth A],
KA [auth B],
KB [auth C],
L [auth A],
LA [auth B],
LB [auth C],
LC [auth D],
M [auth A],
MA [auth B],
MB [auth C],
MC [auth D],
N [auth A],
NA [auth B],
NB [auth C],
O [auth A],
OA [auth B],
OB [auth C],
PA [auth B],
QB [auth D],
UA [auth B],
UB [auth D],
V [auth A],
VB [auth D],
WB [auth D],
X [auth A],
XB [auth D],
Y [auth A],
YB [auth D],
Z [auth A],
ZB [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG
Query on MG

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AB [auth C],
CA [auth A],
F [auth A],
GA [auth B],
SB [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
QWT BindingDB:  7AAG IC50: min: 1.2, max: 4.6 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.168 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.44α = 90
b = 110.82β = 90
c = 161.03γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
xia2data reduction
XSCALEdata 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