SMTL ID : 8xar.1

Structure-Based Design and Optimization of Methionine Adenosyltransferase 2A (MAT2A) Inhibitors with SAM and Compound 54

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.19 Å

Oligo State

homo-dimer

Ligands

2 x YMW: 7-chloranyl-2-ethyl-5-pyridin-3-yl-pyrazolo[3,4-c]quinolin-4-one

YMW.1: 16 residues within 4Å: Chain A: F.32, F.34, Q.204, V.209, G.287, W.288, G.289, R.327, Y.349 Chain B: G.289, A.290, L.329, Q.331, S.345, I.346, F.347 10 PLIP interactions: 7 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:F.32, A:F.32, B:A.290, B:L.329, B:F.347 Hydrogen bonds: A:R.327, A:R.327 Water bridges: A:G.289, A:Y.349 pi-Stacking: A:W.288 YMW.7: 16 residues within 4Å: Chain A: G.289, A.290, L.329, Q.331, S.345, I.346, F.347 Chain B: F.32, F.34, Q.204, V.209, G.287, W.288, G.289, R.327, Y.349 10 PLIP interactions: 7 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:F.32, B:F.32, A:A.290, A:L.329, A:F.347 Hydrogen bonds: B:R.327, B:R.327 Water bridges: B:G.289, B:Y.349 pi-Stacking: B:W.288

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: E.99, A.100, H.103, Q.386 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.99, A:Q.386 Water bridges: A:Q.386 GOL.8: 4 residues within 4Å: Chain B: E.99, A.100, H.103, Q.386 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.99, B:Q.386 Water bridges: B:Q.386

2 x SAM: S-ADENOSYLMETHIONINE(Non-covalent)

SAM.3: 19 residues within 4Å: Chain A: H.43, P.44, D.193, K.195, S.261, R.263, F.264, I.266, D.272 Chain B: A.69, E.84, Q.127, D.130, I.131, G.147, D.148, K.303, I.336 Ligands: CL.6 21 PLIP interactions: 12 interactions with chain A, 9 interactions with chain B Hydrogen bonds: A:D.193, A:S.261, A:R.263, A:D.272, A:D.272, B:E.84, B:Q.127 Water bridges: A:D.45, A:S.220, A:S.261, A:A.273, B:I.131, B:I.131, B:K.303, B:K.303, B:K.303 Salt bridges: A:D.272, B:D.148, B:K.303 pi-Stacking: A:F.264, A:F.264 SAM.9: 19 residues within 4Å: Chain A: A.69, E.84, Q.127, D.130, I.131, G.147, D.148, K.303, I.336 Chain B: H.43, P.44, D.193, K.195, S.261, R.263, F.264, I.266, D.272 Ligands: CL.12 21 PLIP interactions: 12 interactions with chain B, 9 interactions with chain A Hydrogen bonds: B:D.193, B:S.261, B:R.263, B:D.272, B:D.272, A:E.84, A:Q.127 Water bridges: B:D.45, B:S.220, B:S.261, B:A.273, A:I.131, A:I.131, A:K.303, A:K.303, A:K.303 Salt bridges: B:D.272, A:D.148, A:K.303 pi-Stacking: B:F.264, B:F.264

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

EDO.4: 5 residues within 4Å: Chain A: P.341, L.342, I.344, K.364 Chain B: H.215 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:H.215, A:I.344 Water bridges: A:K.364, A:K.364 EDO.5: 4 residues within 4Å: Chain A: D.138, R.139, N.140, D.143 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.140 Water bridges: A:D.143 EDO.10: 5 residues within 4Å: Chain A: H.215 Chain B: P.341, L.342, I.344, K.364 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:I.344, A:H.215 Water bridges: B:K.364, B:K.364 EDO.11: 4 residues within 4Å: Chain B: D.138, R.139, N.140, D.143 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.140 Water bridges: B:D.143

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 5 residues within 4Å: Chain A: H.43, K.195, K.279 Chain B: D.148 Ligands: SAM.3 Ligand excluded by PLIP CL.12: 5 residues within 4Å: Chain A: D.148 Chain B: H.43, K.195, K.279 Ligands: SAM.9 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zheng, J. et al., Structure-Based Design and Optimization of Methionine Adenosyltransferase 2A (MAT2A) Inhibitors with High Selectivity, Brain Penetration, and In Vivo Efficacy. J.Med.Chem. (2024)

Release Date

2024-06-26

Peptides

S-adenosylmethionine synthase isoform type-2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

S-adenosylmethionine synthase isoform type-2

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