SMTL ID : 9mke.1 (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

7 x CA: CALCIUM ION(Non-covalent)

CA.1: 1 residues within 4Å: Chain A: D.44 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.44, H2O.1 CA.2: 4 residues within 4Å: Chain A: E.55, E.104, N.105 Ligands: EDO.11 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.55, A:E.104, H2O.1, H2O.6 CA.3: 6 residues within 4Å: Chain A: E.85, N.86, D.136, Y.137, D.138, D.139 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.85, A:D.136, A:Y.137, A:D.139 CA.4: 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.5: 3 residues within 4Å: Chain A: D.364, T.365, V.366 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.364, A:T.365, H2O.4 CA.6: 1 residues within 4Å: Chain A: E.235 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.235 CA.7: 5 residues within 4Å: Chain A: K.346, E.347, K.376, D.383, H.385 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:K.346, A:D.383, A:H.385, H2O.2

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

PGE.8: 12 residues within 4Å: Chain A: K.71, G.72, K.119, E.120, T.121, G.122, T.150, A.151, N.152, S.222, E.223, R.225 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.71, A:T.150, A:T.150 PGE.9: 14 residues within 4Å: Chain A: E.85, G.88, S.90, Q.110, R.132, D.138, I.141, I.143, Y.157, A.158, T.159, A.214, L.215, E.216 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.88, A:Y.157, A:T.159 Water bridges: A:Q.110, A:Q.110

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

EDO.10: 9 residues within 4Å: Chain A: P.24, H.82, C.131, R.132, K.133, R.134, G.162, A.163, E.164 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.134, A:A.163 Water bridges: A:E.164 EDO.11: 5 residues within 4Å: Chain A: E.55, Y.56, R.59, R.386 Ligands: CA.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.55, A:Y.56, A:R.59, A:R.386, A:R.386 EDO.12: 8 residues within 4Å: Chain A: R.59, V.62, D.63, L.66, L.107, I.112, L.115 Ligands: EDO.13 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.59, A:D.63, A:D.63 EDO.13: 9 residues within 4Å: Chain A: R.59, F.91, S.103, C.106, L.107, C.108, N.111, I.112 Ligands: EDO.12 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.59, A:R.59, A:C.108, A:N.111 Water bridges: A:C.106 EDO.14: 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:L.187, A:K.224 EDO.15: 6 residues within 4Å: Chain A: R.41, W.247, H.251, L.253, A.273, L.378 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.251 EDO.17: 5 residues within 4Å: Chain A: K.180, F.181, R.185, L.215, I.217 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.185 Water bridges: A:K.180 EDO.18: 1 residues within 4Å: Chain A: R.218 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.218, A:R.218

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

01.16: 25 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, R.386 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.48, A:A.61, A:L.68 Hydrogen bonds: A:N.60, A:E.64 Water bridges: A:M.384

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
A

Mucosa-associated lymphoid tissue lymphoma translocation protein 1

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