6F7I

human MALT1(329-728) IN COMPLEX WITH MLT-747


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 

Starting Model: other
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

An allosteric MALT1 inhibitor is a molecular corrector rescuing function in an immunodeficient patient.

Quancard, J.Klein, T.Fung, S.Y.Renatus, M.Hughes, N.Israel, L.Priatel, J.J.Kang, S.Blank, M.A.Viner, R.I.Blank, J.Schlapbach, A.Erbel, P.Kizhakkedathu, J.Villard, F.Hersperger, R.Turvey, S.E.Eder, J.Bornancin, F.Overall, C.M.

(2019) Nat Chem Biol 15: 304-313

  • DOI: https://doi.org/10.1038/s41589-018-0222-1
  • Primary Citation of Related Structures:  
    6F7I, 6H4A

  • PubMed Abstract: 

    MALT1 paracaspase is central for lymphocyte antigen-dependent responses including NF-κB activation. We discovered nanomolar, selective allosteric inhibitors of MALT1 that bind by displacing the side chain of Trp580, locking the protease in an inactive conformation. Interestingly, we had previously identified a patient homozygous for a MALT1 Trp580-to-serine mutation who suffered from combined immunodeficiency. We show that the loss of tryptophan weakened interactions between the paracaspase and C-terminal immunoglobulin MALT1 domains resulting in protein instability, reduced protein levels and functions. Upon binding of allosteric inhibitors of increasing potency, we found proportionate increased stabilization of MALT1-W580S to reach that of wild-type MALT1. With restored levels of stable MALT1 protein, the most potent of the allosteric inhibitors rescued NF-κB and JNK signaling in patient lymphocytes. Following compound washout, MALT1 substrate cleavage was partly recovered. Thus, a molecular corrector rescues an enzyme deficiency by substituting for the mutated residue, inspiring new potential precision therapies to increase mutant enzyme activity in other deficiencies.


  • Organizational Affiliation

    Novartis Institutes for BioMedical Research, Novartis Campus, Basel, Switzerland. jean.quancard@novartis.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mucosa-associated lymphoid tissue lymphoma translocation protein 1
A, B
404Homo 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 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CW5
Query on CW5

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
1-[2-chloranyl-7-[(1~{S})-1-methoxyethyl]pyrazolo[1,5-a]pyrimidin-6-yl]-3-(5-chloranyl-6-pyrrolidin-1-ylcarbonyl-pyridin-3-yl)urea
C20 H21 Cl2 N7 O3
OJTGJRAKRGEDPI-NSHDSACASA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A],
H [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.2α = 90
b = 108.97β = 111.79
c = 73.51γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-02
    Type: Initial release
  • Version 1.1: 2019-02-13
    Changes: Data collection, Database references
  • Version 1.2: 2019-02-27
    Changes: Data collection, Database references
  • Version 1.3: 2024-05-01
    Changes: Data collection, Database references, Refinement description