5LHI

Structure of the KDM1A/CoREST complex with the inhibitor N-[3-(ethoxymethyl)-2-[[4-[[(3R)-pyrrolidin-3-yl]methoxy]phenoxy]methyl]phenyl]-4-methylthieno[3,2-b]pyrrole-5-carboxamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Thieno[3,2-b]pyrrole-5-carboxamides as New Reversible Inhibitors of Histone Lysine Demethylase KDM1A/LSD1. Part 2: Structure-Based Drug Design and Structure-Activity Relationship.

Vianello, P.Sartori, L.Amigoni, F.Cappa, A.Faga, G.Fattori, R.Legnaghi, E.Ciossani, G.Mattevi, A.Meroni, G.Moretti, L.Cecatiello, V.Pasqualato, S.Romussi, A.Thaler, F.Trifiro, P.Villa, M.Botrugno, O.A.Dessanti, P.Minucci, S.Vultaggio, S.Zagarri, E.Varasi, M.Mercurio, C.

(2017) J. Med. Chem. 60: 1693-1715

  • DOI: 10.1021/acs.jmedchem.6b01019
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The balance of methylation levels at histone H3 lysine 4 (H3K4) is regulated by KDM1A (LSD1). KDM1A is overexpressed in several tumor types, thus representing an emerging target for the development of novel cancer therapeutics. We have previously des ...

    The balance of methylation levels at histone H3 lysine 4 (H3K4) is regulated by KDM1A (LSD1). KDM1A is overexpressed in several tumor types, thus representing an emerging target for the development of novel cancer therapeutics. We have previously described ( Part 1, DOI 10.1021.acs.jmedchem.6b01018 ) the identification of thieno[3,2-b]pyrrole-5-carboxamides as novel reversible inhibitors of KDM1A, whose preliminary exploration resulted in compound 2 with biochemical IC 50 = 160 nM. We now report the structure-guided optimization of this chemical series based on multiple ligand/KDM1A-CoRest cocrystal structures, which led to several extremely potent inhibitors. In particular, compounds 46, 49, and 50 showed single-digit nanomolar IC 50 values for in vitro inhibition of KDM1A, with high selectivity in secondary assays. In THP-1 cells, these compounds transcriptionally affected the expression of genes regulated by KDM1A such as CD14, CD11b, and CD86. Moreover, 49 and 50 showed a remarkable anticlonogenic cell growth effect on MLL-AF9 human leukemia cells.


    Organizational Affiliation

    IFOM- The FIRC Institute of Molecular Oncology Foundation , Via Adamello 16, 20139 Milano, Italy.,Department of Biosciences, University of Milan , Via Celoria 26, 20133 Milano, Italy.,Genextra Group, DAC s.r.l. , Via Adamello 16, 20139 Milano, Italy.,Department of Experimental Oncology, Academic Drug Discovery, European Institute of Oncology , Via Adamello 16, 20139 Milano, Italy.,Department of Biology and Biotechnology, University of Pavia , Via Ferrata 1, 27100 Pavia, Italy.,Crystallography Unit, Department of Experimental Oncology, European Institute of Oncology , Via Adamello 16, 20139 Milano, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LYSINE-SPECIFIC HISTONE DEMETHYLASE 1
A
852Homo sapiensMutation(s): 0 
Gene Names: KDM1A (AOF2, KDM1, KIAA0601, LSD1)
EC: 1.-.-.-
Find proteins for O60341 (Homo sapiens)
Go to Gene View: KDM1A
Go to UniProtKB:  O60341
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
REST corepressor 1
B
482Homo sapiensMutation(s): 0 
Gene Names: RCOR1 (KIAA0071, RCOR)
Find proteins for Q9UKL0 (Homo sapiens)
Go to Gene View: RCOR1
Go to UniProtKB:  Q9UKL0
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download SDF File 
Download CCD File 
A
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
6X5
Query on 6X5

Download SDF File 
Download CCD File 
A
~{N}-[3-(ethoxymethyl)-2-[[4-[[(3~{R})-pyrrolidin-3-yl]methoxy]phenoxy]methyl]phenyl]-4-methyl-thieno[3,2-b]pyrrole-5-carboxamide
C29 H33 N3 O4 S
SQSNNQXVJVEDMY-HXUWFJFHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.195 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 120.030α = 90.00
b = 180.370β = 90.00
c = 235.750γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
xia2data scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-02-22
    Type: Initial release
  • Version 1.1: 2017-03-22
    Type: Database references
  • Version 1.2: 2019-10-16
    Type: Data collection