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 

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
  • Primary Citation of Related Structures:  

  • 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 synthesi ...

    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

    WuXi AppTec Co., Ltd., 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China.,Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA. Electronic address: liang.jun@gene.com.,Constellation Pharmaceuticals Inc., 215 First Street, Suite 200, Cambridge, MA 02142, USA.,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 5A
A, B
790Homo sapiensMutation(s): 0 
Gene Names: KDM5A (JARID1A, RBBP2, RBP2)
EC: 1.14.11.-
Find proteins for P29375 (Homo sapiens)
Go to Gene View: KDM5A
Go to UniProtKB:  P29375
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Lysine-specific demethylase 5A
G
10N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
90V
Query on 90V

Download SDF File 
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
NI
Query on NI

Download SDF File 
Download CCD File 
A, B
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
G
L-PEPTIDE LINKINGC4 H9 N O2

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.232 
  • Space Group: P 31
Unit Cell:
Length (Å)Angle (°)
a = 159.615α = 90.00
b = 159.615β = 90.00
c = 92.071γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PDB_EXTRACTdata extraction
PHASERphasing
PHENIXrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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