9MKC | pdb_00009mkc

Crystal structure of MALT1 in complex with an allosteric inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.305 (Depositor), 0.293 (DCC) 
  • R-Value Work: 
    0.281 (Depositor), 0.273 (DCC) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Accelerated In Silico Discovery of SGR-1505 : A Potent MALT1 Allosteric Inhibitor for the Treatment of Mature B-Cell Malignancies.

Nie, Z.Trzoss, M.Placzek, A.T.Trzoss, L.Krilov, G.Feng, S.Lawrenz, M.Ye, M.Marshall, N.Dingley, K.H.Pelletier, R.D.Lai, W.G.Bell, J.A.Tang, H.Devine, P.Liu, Z.Skrdla, P.Shimanovich, R.Liu, M.Wang, R.Xu, X.Bhat, S.Bos, P.H.Abel, R.Akinsanya, K.Yin, W.

(2025) J Med Chem 68: 23977-23992

  • DOI: https://doi.org/10.1021/acs.jmedchem.5c01494
  • Primary Citation of Related Structures:  
    9MKC, 9MKD, 9MKE

  • PubMed Abstract: 

    MALT1 is a key component of the CARD11-BCL10-MALT1 (CBM) complex downstream from BTK on the B-cell receptor signaling pathway. It is a key mediator of NF-κB signaling and considered a potential therapeutic target for several subtypes of non-Hodgkin's B-cell lymphomas. By applying advanced physics-based modeling techniques, including combining free energy calculations with machine learning methods and a chemistry-aware compound enumeration workflow, extensive sets of de novo design ideas were explored to quickly identify a novel hit series. Multiparameter optimization allowed efficient prioritization of molecules with good potency and drug-like properties during lead optimization, which led to the discovery of a highly potent MALT1 inhibitor, SGR-1505 , with a well-balanced property profile. It demonstrated strong antitumor activity alone and in combination with BTK inhibitor in multiple in vivo B-cell lymphoma xenograft models and progressed to a phase 1 clinical trial in patients with mature B-cell neoplasms.


  • Organizational Affiliation
    • Schrödinger Inc., San Diego, California 92121, United States.

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
386Homo 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
A1BM0 (Subject of Investigation/LOI)
Query on A1BM0

Download Ideal Coordinates CCD File 
G [auth A],
L [auth B]
N-[(8R)-2-chloro-7-(propan-2-yl)pyrazolo[1,5-a]pyrimidin-6-yl]-N'-[5-chloro-6-(2H-1,2,3-triazol-2-yl)pyridin-3-yl]urea
C17 H15 Cl2 N9 O
GSQOTVHUYJQPDR-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
H [auth B]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
H [auth B],
I [auth B],
J [auth B],
K [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.305 (Depositor), 0.293 (DCC) 
  • R-Value Work:  0.281 (Depositor), 0.273 (DCC) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.66α = 90
b = 77.151β = 93.59
c = 92.47γ = 90
Software Package:
Software NamePurpose
PRIME-Xrefinement
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2025-10-29 
  • Deposition Author(s): Bell, J.A.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-29
    Type: Initial release
  • Version 1.1: 2025-12-10
    Changes: Database references