4UXN

LSD1(KDM1A)-CoREST in complex with Z-Pro derivative of MC2580

PDB DOI: https://doi.org/10.2210/pdb4UXN/pdb

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

Deposited: 2014-08-27 Released: 2015-02-25
Deposition Author(s): Rodriguez, V., Valente, S., Stazi, G., Lucidi, A., Mercurio, C., Vianello, P., Ciossani, G., Mattevi, A., Botrugno, O.A., Dessanti, P., Minucci, S., Varasi, M., Mai, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.85 Å
R-Value Free: 0.215
R-Value Work: 0.206
R-Value Observed: 0.206

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Pyrrole- and Indole-Containing Tranylcypromine Derivatives as Novel Lysine-Specific Demethylase 1 Inhibitors Active on Cancer Cells

Rodriguez, V., Valente, S., Rovida, S., Rotili, D., Stazi, G., Lucidi, A., Ciossani, G., Mattevi, A., Botrugno, O.A., Dessanti, P., Mercurio, C., Vianello, P., Minucci, S., Varasi, M., Mai, A.

(2015) ChemMedChem 6: 665-670

DOI: https://doi.org/10.1039/C4MD00507D

Macromolecule Content

Total Structure Weight: 147.28 kDa
Atom Count: 6,374
Modelled Residue Count: 799
Deposited Residue Count: 1,334
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	852	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD 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]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
M8A Query on M8A Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	benzyl (2R)-2-{[4-(3-oxopropyl)phenyl]carbamoyl}pyrrolidine-1-carboxylate C₂₂ H₂₄ N₂ O₄ ACUUWDZYZLDIFD-HXUWFJFHSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.85 Å
R-Value Free: 0.215
R-Value Work: 0.206
R-Value Observed: 0.206
Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.98	α = 90
b = 177.76	β = 90
c = 233.72	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-02-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-02-25
Type: Initial release
Version 1.1: 2018-06-13
Changes: Data collection, Database references
Version 1.2: 2018-06-20
Changes: Advisory, Data collection, Derived calculations
Version 1.3: 2019-02-20
Changes: Advisory, Data collection, Derived calculations
Version 1.4: 2024-01-10
Changes: Data collection, Database references, Other, Refinement description