SMTL ID : 9mkd.1

Crystal structure of MALT1 in complex with an allosteric inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

homo-dimer

Ligands

11 x CA: CALCIUM ION(Non-covalent)

CA.1: 3 residues within 4Å: Chain A: E.55, E.104, N.105 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.55, A:E.104, H2O.5, H2O.5 CA.2: 5 residues within 4Å: Chain A: E.85, N.86, D.136, Y.137, D.139 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.85, A:D.136, A:Y.137, A:D.139, H2O.5 CA.3: 5 residues within 4Å: Chain A: V.31, D.32, H.170, G.172, N.175 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.32, A:H.170, A:G.172, H2O.1, H2O.3 CA.4: 3 residues within 4Å: Chain A: D.364, T.365, V.366 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.364, A:T.365 CA.5: 4 residues within 4Å: Chain A: K.346, K.376, D.383, H.385 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:K.346, A:D.383, A:D.383, A:H.385, H2O.1 CA.8: 1 residues within 4Å: Chain A: N.89 No protein-ligand interaction detected (PLIP) CA.9: 2 residues within 4Å: Chain B: L.67, D.70 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:L.67, B:D.70, H2O.9, H2O.10 CA.10: 4 residues within 4Å: Chain B: E.55, R.59, E.104, N.105 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.55, B:E.104, H2O.10, H2O.10 CA.11: 5 residues within 4Å: Chain B: E.85, N.86, D.136, D.139, T.140 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.85, B:D.136, B:D.139, B:T.140, H2O.9 CA.12: 5 residues within 4Å: Chain B: V.31, D.32, H.170, G.172, N.175 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:H.170, B:G.172, H2O.5, H2O.6, H2O.7 CA.13: 2 residues within 4Å: Chain B: D.364, T.365 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.364, B:T.365

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.6: 7 residues within 4Å: Chain A: R.41, W.247, H.251, E.252, L.253, A.273, L.378 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.41 Water bridges: A:S.276

2 x 01: (9R)-2-chloro-N-[5-chloro-6-(2H-1,2,3-triazol-2-yl)pyridin-3-yl]-8,8-dimethyl-7,8-dihydro-6H-pyrazolo[1,5-a]pyrrolo[2,3-e]pyrimidine-6-carboxamide

01.7: 24 residues within 4Å: Chain A: V.11, A.12, L.13, K.46, V.47, V.48, L.50, L.53, Y.56, E.57, N.60, A.61, E.64, F.65, L.68, Q.246, W.247, A.250, H.251, Q.343, I.379, L.382, M.384, H.385 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.48, A:A.61, A:A.250, A:I.379 Hydrogen bonds: A:N.60, A:E.64 Water bridges: A:M.384 01.14: 24 residues within 4Å: Chain B: V.11, A.12, L.13, K.46, V.48, L.50, L.53, Y.56, E.57, N.60, A.61, E.64, F.65, L.68, Q.246, W.247, A.250, H.251, Q.343, K.344, I.379, L.382, M.384, H.385 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:A.61, B:L.68, B:Q.246, B:A.250 Hydrogen bonds: B:N.60, B:E.64

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nie, Z. et al., Accelerated In Silico Discovery of SGR-1505 : A Potent MALT1 Allosteric Inhibitor for the Treatment of Mature B-Cell Malignancies. J.Med.Chem. (2025)

Release Date

2025-10-29

Peptides

Mucosa-associated lymphoid tissue lymphoma translocation protein 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Mucosa-associated lymphoid tissue lymphoma translocation protein 1

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