	235,183 Structures from the PDB
	1,068,577 Computed Structure Models (CSM)

4UVC|pdb_00004uvc

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

PDB DOI: https://doi.org/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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free:
0.241 (Depositor), 0.240 (DCC)
R-Value Work:
0.210 (Depositor), 0.210 (DCC)
R-Value Observed:
0.211 (Depositor)

Starting Model:experimental
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Ligand Structure Quality Assessment

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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 Search on PubMed
DOI: https://doi.org/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.

Organizational Affiliation

Drug Discovery Unit, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy. Electronic address: paola.vianello@ieo.eu.

Macromolecule Content

Total Structure Weight: 148.95 kDa
Atom Count: 6,361
Modelled Residue Count: 799
Deposited Residue Count: 1,354
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LYSINE-SPECIFIC HISTONE DEMETHYLASE 1A	A	872	Homo sapiens	Mutation(s): 0 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 GTEx: ENSG00000004487
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O60341
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
REST COREPRESSOR 1	B	482	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UKL0 (Homo sapiens) Explore Q9UKL0 Go to UniProtKB: Q9UKL0
PHAROS: Q9UKL0 GTEx: ENSG00000089902
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9UKL0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
D52 Query on D52 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	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		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.241 (Depositor), 0.240 (DCC)
R-Value Work: 0.210 (Depositor), 0.210 (DCC)
R-Value Observed: 0.211 (Depositor)

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

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-09-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-09-10
Type: Initial release
Version 1.1: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Other, Refinement description