SMTL ID : 9mke.2 (1 other biounit)

Crystal structure of MALT1 in complex with an allosteric inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.34 Å

Oligo State

monomer

Ligands

10 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 5 residues within 4Å: Chain A: F.181, R.185, I.217, R.218, S.219 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.185, A:R.185, A:S.219 EDO.8: 4 residues within 4Å: Chain A: L.208, Q.213, A.214, L.215 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.213 EDO.9: 8 residues within 4Å: Chain A: R.59, V.62, D.63, L.66, L.107, I.112, L.115 Ligands: EDO.15 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.59, A:D.63, A:D.63 EDO.10: 1 residues within 4Å: Chain A: D.44 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.44 EDO.11: 6 residues within 4Å: Chain A: H.251, E.252, L.253, A.273, L.378 Ligands: PGE.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.251 EDO.12: 3 residues within 4Å: Chain A: K.133, R.134, N.135 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.134, A:N.135 Water bridges: A:K.133 EDO.13: 4 residues within 4Å: Chain A: N.86, F.87, N.89, F.91 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.86, A:N.86 EDO.14: 8 residues within 4Å: Chain A: P.24, H.82, K.133, R.134, G.162, A.163, E.164, A.165 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.163, A:E.164 Water bridges: A:Q.161, A:A.165 EDO.15: 8 residues within 4Å: Chain A: R.59, C.106, L.107, C.108, N.111, I.112, L.115 Ligands: EDO.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.59, A:R.59, A:C.108 EDO.16: 7 residues within 4Å: Chain A: R.185, L.186, L.187, E.188, K.224, R.225, A.226 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.187, A:R.225, A:R.225

5 x CA: CALCIUM ION(Non-covalent)

CA.2: 6 residues within 4Å: Chain A: V.31, D.32, H.170, G.172, L.173, N.175 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.170, A:G.172, H2O.1, H2O.1, H2O.5 CA.3: 4 residues within 4Å: Chain A: D.364, T.365, V.366, E.367 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.364, A:T.365, H2O.5 CA.4: 2 residues within 4Å: Chain A: L.67, D.70 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:L.67, A:D.70, H2O.6, H2O.6, H2O.6 CA.5: 4 residues within 4Å: Chain A: E.55, R.59, E.104, N.105 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.55, A:E.104, H2O.5, H2O.5, H2O.5 CA.6: 5 residues within 4Å: Chain A: E.85, N.86, D.136, Y.137, D.139 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.136, A:Y.137, A:D.139, H2O.1, H2O.6

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

PGE.7: 13 residues within 4Å: Chain A: Y.34, T.37, R.41, V.47, V.48, S.49, W.247, H.251, A.273, E.274, F.275, S.276 Ligands: EDO.11 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.41, A:R.41, A:E.274 Water bridges: A:R.41, A:S.49

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

01.17: 24 residues within 4Å: Chain A: 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 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.48, A:A.61, A:L.68 Hydrogen bonds: A:N.60, A: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: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Mucosa-associated lymphoid tissue lymphoma translocation protein 1

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