6P5V

Structure of DCN1 bound to N-((4S,5S)-7-ethyl-4-(4-fluorophenyl)-3-methyl-6-oxo-1-phenyl-4,5,6,7-tetrahydro-1H-pyrazolo[3,4-b]pyridin-5-yl)-3-methylbenzamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.398 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Discovery of Novel Pyrazolo-Pyridone DCN1 Inhibitors Controlling Cullin Neddylation.

Kim, H.S.Hammill, J.T.Scott, D.C.Chen, Y.Min, J.Rector, J.Singh, B.Schulman, B.A.Guy, R.K.

(2019) J.Med.Chem. --: --

  • DOI: 10.1021/acs.jmedchem.9b00410
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Chemical control of cullin neddylation is attracting increased attention based largely on the successes of the NEDD8-activating enzyme (E1) inhibitor Pevonedistat. Recently reported chemical probes enable selective and time-dependent inhibition of do ...

    Chemical control of cullin neddylation is attracting increased attention based largely on the successes of the NEDD8-activating enzyme (E1) inhibitor Pevonedistat. Recently reported chemical probes enable selective and time-dependent inhibition of downstream members of the neddylation tri-enzymatic cascade including the co-E3, DCN1. In this work, we report the optimization of a novel class of small molecule inhibitors of the DCN1-UBE2M interaction. Rational X-ray co-structure enabled optimization afforded a 25-fold improvement in potency relative to the initial screening hit. The potency gains are largely attributed to additional hydrophobic interactions mimicking the N-terminal acetyl group that drives binding of UBE2M to DCN1. The compounds inhibit the protein-protein interaction, block NEDD8 transfer in biochemical assays, engage DCN1 in cells, and selectively reduce the steady-state neddylation of Cul1 and Cul3 in two squamous carcinoma cell lines harboring DCN1 amplification.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysozyme,DCN1-like protein 1 fusion
A
384Homo sapiensEnterobacteria phage T4
This entity is chimeric
Mutation(s): 0 
Gene Names: DCUN1D1 (DCN1, DCUN1L1, RP42, SCCRO), e
EC: 3.2.1.17
Find proteins for Q96GG9 (Homo sapiens)
Go to Gene View: DCUN1D1
Go to UniProtKB:  Q96GG9
Find proteins for D9IEF7 (Enterobacteria phage T4)
Go to UniProtKB:  D9IEF7
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
O37
Query on O37

Download SDF File 
Download CCD File 
A
N-[(4S,5S)-1-[(1S)-cyclohex-3-en-1-yl]-7-ethyl-4-(4-fluorophenyl)-3-methyl-6-oxo-4,5,6,7-tetrahydro-1H-pyrazolo[3,4-b]pyridin-5-yl]-3-methylbenzamide
C29 H31 F N4 O2
DRGYLPYZJGVISN-AFESJLNVSA-N
 Ligand Interaction
MPD
Query on MPD

Download SDF File 
Download CCD File 
A
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.398 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.171 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 35.310α = 90.00
b = 96.985β = 106.09
c = 60.072γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer InstituteUnited States--

Revision History 

  • Version 1.0: 2019-09-11
    Type: Initial release