Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 148.95 kDa 
• Atom Count: 6361 
• Modelled Residue Count: 799 
• Deposited Residue Count: 1354 
• Unique protein chains: 2

4UVC

LSD1(KDM1A)-CoREST in complex with 1-Phenyl-Tranylcypromine

• PDB DOI: 10.2210/pdb4UVC/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2014-08-05 Released: 2014-09-10 
• Deposition Author(s): Vianello, P., Botrugno, O., Cappa, A., Ciossani, G., Dessanti, P., Mai, A., Mattevi, A., Meroni, G., Minucci, S., Thaler, F., Tortorici, M., Trifiro, P., Valente, S., Villa, M., Varasi, M., Mercurio, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.241 
• R-Value Work: 0.210 
• R-Value Observed: 0.211 

Literature

Synthesis, Biological Activity and Mechanistic Insights of 1-Substituted Cyclopropylamine Derivatives: A Novel Class of Irreversible Inhibitors of Histone Demethylase Kdm1A.

Vianello, P., Botrugno, O.A., Cappa, A., Ciossani, G., Dessanti, P., Mai, A., Mattevi, A., Meroni, G., Minucci, S., Thaler, F., Tortorici, M., Trifiro, P., Valente, S., Villa, M., Varasi, M., Mercurio, C.

(2014) Eur J Med Chem 86C: 352

• PubMed: 25173853 
• DOI: 10.1016/j.ejmech.2014.08.068
• Primary Citation of Related Structures:  
  4UV8, 4UV9, 4UVA, 4UVB, 4UVC


• PubMed Abstract: 
  

Histone demethylase KDM1A (also known as LSD1) has become an attractive therapeutic target for the treatment of cancer as well as other disorders such as viral infections. We report on the synthesis of compounds derived from the expansion of tranylcypromine as a chemical scaffold for the design of novel demethylase inhibitors. These compounds, which are substituted on the cyclopropyl core moiety, were evaluated for their ability to inhibit KDM1A in vitro as well as to function in cells by modulating the expression of Gfi-1b, a well recognized KDM1A target gene. The molecules were all found to covalently inhibit KDM1A and to become increasingly selective against human monoamine oxidases MAO A and MAO B through the introduction of bulkier substituents on the cyclopropylamine ring. Structural and biochemical analysis of selected trans isomers showed that the two stereoisomers are endowed with similar inhibitory activities against KDM1A, but form different covalent adducts with the FAD co-enzyme.

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Organizational Affiliation: 

Drug Discovery Unit, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LYSINE-SPECIFIC HISTONE DEMETHYLASE 1A	A	872	Homo sapiens	Mutation(s): 0  Gene Names: KDM1A, AOF2, KDM1, KIAA0601, LSD1 EC: 1 (PDB Primary Data), 1.14.99.66 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O60341 (Homo sapiens) Explore O60341  Go to UniProtKB:  O60341
PHAROS:  O60341

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
REST COREPRESSOR 1	B	482	Homo sapiens	Mutation(s): 0  Gene Names: RCOR1, KIAA0071, RCOR
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UKL0 (Homo sapiens) Explore Q9UKL0  Go to UniProtKB:  Q9UKL0
PHAROS:  Q9UKL0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
D52	C [auth A]	[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4S)-5-[5-[(1S)-1-azanyl-1,3-diphenyl-propyl]-7,8-dimethyl-2,4-bis(oxidanylidene)-4aH-benzo[g]pteridin-10-yl]-2,3,4-tris(oxidanyl)pentyl] hydrogen phosphate C42 H50 N10 O15 P2 AZOWZKANNHCUOJ-VIIZLGSKSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.241 
• R-Value Work: 0.210 
• R-Value Observed: 0.211 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.96	α = 90
b = 179.09	β = 90
c = 234.8	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-08-05 
• Released Date: 2014-09-10 
Deposition Author(s): Vianello, P., Botrugno, O., Cappa, A., Ciossani, G., Dessanti, P., Mai, A., Mattevi, A., Meroni, G., Minucci, S., Thaler, F., Tortorici, M., Trifiro, P., Valente, S., Villa, M., Varasi, M., Mercurio, C.

Revision History  

• Version 1.0: 2014-09-10
  Type: Initial release