5L3E

LSD1-CoREST1 in complex with quinazoline-derivative reversible inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Polymyxins and quinazolines are LSD1/KDM1A inhibitors with unusual structural features.

Speranzini, V.Rotili, D.Ciossani, G.Pilotto, S.Marrocco, B.Forgione, M.Lucidi, A.Forneris, F.Mehdipour, P.Velankar, S.Mai, A.Mattevi, A.

(2016) Sci Adv 2: e1601017-e1601017

  • DOI: 10.1126/sciadv.1601017
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Because of its involvement in the progression of several malignant tumors, the histone lysine-specific demethylase 1 (LSD1) has become a prominent drug target in modern medicinal chemistry research. We report on the discovery of two classes of noncov ...

    Because of its involvement in the progression of several malignant tumors, the histone lysine-specific demethylase 1 (LSD1) has become a prominent drug target in modern medicinal chemistry research. We report on the discovery of two classes of noncovalent inhibitors displaying unique structural features. The antibiotics polymyxins bind at the entrance of the substrate cleft, where their highly charged cyclic moiety interacts with a cluster of positively charged amino acids. The same site is occupied by quinazoline-based compounds, which were found to inhibit the enzyme through a most peculiar mode because they form a pile of five to seven molecules that obstruct access to the active center. These data significantly indicate unpredictable strategies for the development of epigenetic inhibitors.


    Organizational Affiliation

    Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy.,Department of Experimental Oncology, European Institute of Oncology, via Adamello 16, 20139 Milan, Italy.,European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, Cambridgeshire CB10 1SD, U.K.,Department of Drug Chemistry and Technologies, Sapienza University of Rome, P. le A. Moro 5, 00185 Rome, Italy.,Department of Drug Chemistry and Technologies, Sapienza University of Rome, P. le A. Moro 5, 00185 Rome, Italy.; Pasteur Institute-Cenci Bolognetti Foundation, Sapienza University of Rome, P. le A. Moro 5, 00185 Rome, Italy.,Department of Drug Chemistry and Technologies, Sapienza University of Rome, P. le A. Moro 5, 00185 Rome, Italy.; Center for Life Nano Science@Sapienza, Italian Institute of Technology, Viale Regina Elena 291, 00161 Rome, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysine-specific histone demethylase 1A
A
730Homo 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
178Homo 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
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
FAD
Query on FAD

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Download CCD File 
A
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
E11
Query on E11

Download SDF File 
Download CCD File 
A
N~4~-(1-benzylpiperidin-4-yl)-N~2~-[3-(dimethylamino)propyl]-6,7-dimethoxyquinazoline-2,4-diamine
C27 H38 N6 O2
YYFDMPHIONBOKZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.200 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 116.570α = 90.00
b = 178.400β = 90.00
c = 233.780γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PHASERphasing
iMOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
AIRCItalyIG-15208
MIURItalyProgetto Bandiera Epigenomica - EPIGEN
ItalyRF-2010-2318330
ItalySapienza Award Project 2014
ItalyIIT-Sapienza Project
AIRC-Fondazione CariploItalyTRIDEO Id. 17515
MIURItalyPRIN 2012CTAYSY
EUFP7 Projects BLUEPRINT/282510
A-PARADDISEA-PARADDISE/602080
Giovanni Armenise-Harvard foundationUnited StatesCareer development award 2013
MIURItalyProgramma Giovani Ricercatori Rita Levi-Montalcini 2013

Revision History 

  • Version 1.0: 2016-09-21
    Type: Initial release
  • Version 1.1: 2016-10-05
    Type: Database references