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


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)  |  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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
D68
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

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

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AA [auth A] , AB [auth C] , AC [auth D] , BA [auth A] , BB [auth C] , BC [auth D] , CC [auth D] , DC [auth D] , 
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



Entry History 

Deposition Data

Revision History  (Full details and data files)

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