7AK1

Human MALT1(329-729) in complex with a chromane urea containing inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Discovery of Potent, Highly Selective, and In Vivo Efficacious, Allosteric MALT1 Inhibitors by Iterative Scaffold Morphing.

Pissot Soldermann, C.Simic, O.Renatus, M.Erbel, P.Melkko, S.Wartmann, M.Bigaud, M.Weiss, A.McSheehy, P.Endres, R.Santos, P.Blank, J.Schuffenhauer, A.Bold, G.Buschmann, N.Zoller, T.Altmann, E.Manley, P.W.Dix, I.Buchdunger, E.Scesa, J.Quancard, J.Schlapbach, A.Bornancin, F.Radimerski, T.Regnier, C.H.

(2020) J Med Chem 63: 14576-14593

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c01245
  • Primary Citation of Related Structures:  
    7AK0, 7AK1

  • PubMed Abstract: 

    MALT1 plays a central role in immune cell activation by transducing NF-κB signaling, and its proteolytic activity represents a key node for therapeutic intervention. Two cycles of scaffold morphing of a high-throughput biochemical screening hit resulted in the discovery of MLT-231, which enabled the successful pharmacological validation of MALT1 allosteric inhibition in preclinical models of humoral immune responses and B-cell lymphomas. Herein, we report the structural activity relationships (SARs) and analysis of the physicochemical properties of a pyrazolopyrimidine-derived compound series. In human T-cells and B-cell lymphoma lines, MLT-231 potently and selectively inhibits the proteolytic activity of MALT1 in NF-κB-dependent assays. Both in vitro and in vivo profiling of MLT-231 support further optimization of this in vivo tool compound toward preclinical characterization.


  • Organizational Affiliation

    Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002 Basel, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mucosa-associated lymphoid tissue lymphoma translocation protein 1404Homo sapiensMutation(s): 0 
Gene Names: MALT1MLT
EC: 3.4.22
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UDY8 (Homo sapiens)
Explore Q9UDY8 
Go to UniProtKB:  Q9UDY8
PHAROS:  Q9UDY8
GTEx:  ENSG00000172175 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UDY8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
RJH (Subject of Investigation/LOI)
Query on RJH

Download Ideal Coordinates CCD File 
B [auth A]1-(3-chloranyl-4-methoxy-phenyl)-3-[7-[(3~{S})-3-(methoxymethyl)morpholin-4-yl]-2-methyl-pyrazolo[1,5-a]pyrimidin-6-yl]urea
C21 H25 Cl N6 O4
IUORVTKNCDNHNC-HNNXBMFYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.199 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.32α = 90
b = 56.33β = 99.77
c = 79.783γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
BUSTERphasing
XDSdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2020-12-09 
  • Deposition Author(s): Renatus, M.

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-09
    Type: Initial release
  • Version 1.1: 2020-12-23
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Database references, Refinement description