5V9T

Crystal structure of selective pyrrolidine amide KDM5a inhibitor N-{(3R)-1-[3-(propan-2-yl)-1H-pyrazole-5-carbonyl]pyrrolidin-3-yl}cyclopropanecarboxamide (compound 48)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.235 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

From a novel HTS hit to potent, selective, and orally bioavailable KDM5 inhibitors.

Liang, J.Labadie, S.Zhang, B.Ortwine, D.F.Patel, S.Vinogradova, M.Kiefer, J.R.Mauer, T.Gehling, V.S.Harmange, J.C.Cummings, R.Lai, T.Liao, J.Zheng, X.Liu, Y.Gustafson, A.Van der Porten, E.Mao, W.Liederer, B.M.Deshmukh, G.An, L.Ran, Y.Classon, M.Trojer, P.Dragovich, P.S.Murray, L.

(2017) Bioorg Med Chem Lett 27: 2974-2981

  • DOI: 10.1016/j.bmcl.2017.05.016
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • A high-throughput screening (HTS) of the Genentech/Roche library identified a novel, uncharged scaffold as a KDM5A inhibitor. Lacking insight into the binding mode, initial attempts to improve inhibitor potency failed to improve potency, and synthesis of analogs was further hampered by the presence of a C-C bond between the pyrrolidine and pyridine ...

    A high-throughput screening (HTS) of the Genentech/Roche library identified a novel, uncharged scaffold as a KDM5A inhibitor. Lacking insight into the binding mode, initial attempts to improve inhibitor potency failed to improve potency, and synthesis of analogs was further hampered by the presence of a C-C bond between the pyrrolidine and pyridine. Replacing this with a C-N bond significantly simplified synthesis, yielding pyrazole analog 35, of which we obtained a co-crystal structure with KDM5A. Using structure-based design approach, we identified 50 with improved biochemical, cell potency and reduced MW and lower lipophilicity (LogD) compared with the original hit. Furthermore, 50 showed lower clearance than 9 in mice. In combination with its remarkably low plasma protein binding (PPB) in mice (40%), oral dosing of 50 at 5mg/kg resulted in unbound C max ∼2-fold of its cell potency (PC9 H3K4Me3 0.96μM), meeting our criteria for an in vivo tool compound from a new scaffold.


    Organizational Affiliation

    Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysine-specific demethylase 5AA, B790Homo sapiensMutation(s): 0 
Gene Names: KDM5AJARID1ARBBP2RBP2
EC: 1.14.11 (PDB Primary Data), 1.14.11.67 (UniProt)
Find proteins for P29375 (Homo sapiens)
Explore P29375 
Go to UniProtKB:  P29375
NIH Common Fund Data Resources
PHAROS  P29375
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Lysine-specific demethylase 5AG10Homo sapiensMutation(s): 0 
Gene Names: KDM5AJARID1ARBBP2RBP2
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
90V
Query on 90V

Download CCD File 
A, B
N-{(3R)-1-[3-(propan-2-yl)-1H-pyrazole-5-carbonyl]pyrrolidin-3-yl}cyclopropanecarboxamide
C15 H22 N4 O2
CXEXTVGTDZRKJS-LLVKDONJSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

Download CCD File 
A, B
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.235 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 159.615α = 90
b = 159.615β = 90
c = 92.071γ = 120
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-05-10
    Type: Initial release
  • Version 1.1: 2017-06-14
    Changes: Database references