7PAW | pdb_00007paw

MALT1 in complex with compound 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 
    0.235 (Depositor), 0.214 (DCC) 
  • R-Value Work: 
    0.200 (Depositor), 0.215 (DCC) 
  • R-Value Observed: 
    0.202 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Discovery and optimization of cyclohexane-1,4-diamines as allosteric MALT1 inhibitors.

Schiesser, S.Hajek, P.Pople, H.E.Kack, H.Oster, L.Cox, R.J.

(2021) Eur J Med Chem 227: 113925-113925

  • DOI: https://doi.org/10.1016/j.ejmech.2021.113925
  • Primary Citation Related Structures: 
    7PAV, 7PAW

  • PubMed Abstract: 

    Inhibition of mucosa-associated lymphoid tissue lymphoma translocation protein-1 (MALT1) is a promising strategy to modulate NF-κB signaling, with the potential to treat B-cell lymphoma and autoimmune diseases. We describe the discovery and optimization of (1s,4s)-N,N'-diaryl cyclohexane-1,4-diamines, a novel series of allosteric MALT1 inhibitors, resulting in compound 8 with single digit micromolar cell potency. X-ray analysis confirms that this compound binds to an induced allosteric site in MALT1. Compound 8 is highly selective and has an excellent in vivo rat PK profile with low clearance and high oral bioavailability, making it a promising lead for further optimization.


  • Organizational Affiliation
    • Department of Medicinal Chemistry, Research and Early Development, Respiratory & Immunology (R&I), BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 43183, Mölndal, Sweden. Electronic address: stefan.schiesser@astrazeneca.com.

Macromolecule Content 

  • Total Structure Weight: 88.75 kDa 
  • Atom Count: 5,724 
  • Modeled Residue Count: 713 
  • Deposited Residue Count: 776 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Mucosa-associated lymphoid tissue lymphoma translocation protein 1
A, B
388Homo sapiensMutation(s): 4 
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
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6IT
(Subject of Investigation/LOI)

Query on 6IT



Download:Ideal Coordinates CCD File
C [auth B]~{N}1-(3-chloranyl-[1,2,4]triazolo[4,3-b]pyridazin-6-yl)-~{N}4-[2-(trifluoromethyl)pyrimidin-4-yl]cyclohexane-1,4-diamine
C16 H16 Cl F3 N8
ONWCUJRODWUZTD-AOOOYVTPSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
6IT BindingDB:  7PAW IC50: min: 300, max: 3200 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free:  0.235 (Depositor), 0.214 (DCC) 
  • R-Value Work:  0.200 (Depositor), 0.215 (DCC) 
  • R-Value Observed: 0.202 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.45α = 90
b = 74.97β = 93.87
c = 106.87γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-17
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description