SMTL ID : 8xb0.1

Structure-Based Design and Optimization of Methionine Adenosyltransferase 2A (MAT2A) Inhibitors with SAM and Compound 292

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.12 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 3 residues within 4Å: Chain A: K.102, Y.115, K.116 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.102 Water bridges: A:K.102 EDO.2: 5 residues within 4Å: Chain A: R.233, H.257, L.258, P.260 Chain B: V.338 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.233, A:H.257 Water bridges: A:L.258 EDO.3: 5 residues within 4Å: Chain A: K.242, A.243, V.244, V.245, P.246 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.245 Water bridges: A:A.247 EDO.12: 3 residues within 4Å: Chain B: K.102, Y.115, K.116 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.102 Water bridges: B:K.102 EDO.13: 5 residues within 4Å: Chain A: V.338 Chain B: R.233, H.257, L.258, P.260 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.233, B:H.257 Water bridges: B:L.258 EDO.14: 5 residues within 4Å: Chain B: K.242, A.243, V.244, V.245, P.246 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.245 Water bridges: B:A.247

2 x YN8: 7-chloranyl-5-(2-cyclopropylpyridin-3-yl)-8-fluoranyl-2-methyl-pyrazolo[3,4-c]quinolin-4-one

YN8.4: 18 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, Y.349 Ligands: YN8.15 12 PLIP interactions: 6 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:A.290, B:L.329, B:F.347, B:F.347, B:F.347, B:Y.349, A:F.32, A:F.32 Hydrogen bonds: A:R.327, A:R.327 Water bridges: A:G.289, A:Y.349 YN8.15: 18 residues within 4Å: Chain A: G.289, A.290, L.329, Q.331, S.345, I.346, F.347, Y.349 Chain B: F.32, F.34, Q.204, V.209, G.287, W.288, G.289, R.327, Y.349 Ligands: YN8.4 12 PLIP interactions: 6 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:F.32, B:F.32, A:A.290, A:L.329, A:F.347, A:F.347, A:F.347, A:Y.349 Hydrogen bonds: B:R.327, B:R.327 Water bridges: B:G.289, B:Y.349

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

SAM.5: 21 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.8, CL.10, NA.11 20 PLIP interactions: 11 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:E.84, B:Q.127 Water bridges: A:S.220, A:S.261, A:A.273, B:I.131, B:I.131, 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.16: 21 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.19, CL.21, NA.22 20 PLIP interactions: 11 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:E.84, A:Q.127 Water bridges: B:S.220, B:S.261, B:A.273, A:I.131, A:I.131, 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

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

CL.6: 3 residues within 4Å: Chain A: T.160, E.161, E.162 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain A: D.63, R.88 Ligand excluded by PLIP CL.8: 5 residues within 4Å: Chain B: A.69, K.299, K.303 Ligands: SAM.5, NA.11 Ligand excluded by PLIP CL.9: 1 residues within 4Å: Chain A: E.161 Ligand excluded by PLIP CL.10: 6 residues within 4Å: Chain A: H.43, K.195, K.279 Chain B: D.148 Ligands: SAM.5, NA.11 Ligand excluded by PLIP CL.17: 3 residues within 4Å: Chain B: T.160, E.161, E.162 Ligand excluded by PLIP CL.18: 2 residues within 4Å: Chain B: D.63, R.88 Ligand excluded by PLIP CL.19: 5 residues within 4Å: Chain A: A.69, K.299, K.303 Ligands: SAM.16, NA.22 Ligand excluded by PLIP CL.20: 1 residues within 4Å: Chain B: E.161 Ligand excluded by PLIP CL.21: 6 residues within 4Å: Chain A: D.148 Chain B: H.43, K.195, K.279 Ligands: SAM.16, NA.22 Ligand excluded by PLIP

2 x NA: SODIUM ION(Non-functional Binders)

NA.11: 4 residues within 4Å: Chain B: K.299 Ligands: SAM.5, CL.8, CL.10 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:K.299, B:K.299 Water bridges: B:D.148, B:D.305, A:R.278, A:R.278 NA.22: 4 residues within 4Å: Chain A: K.299 Ligands: SAM.16, CL.19, CL.21 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:K.299 Water bridges: A:D.148, A:D.305, A:D.305, B:D.272, B:D.272, B:R.278, B:R.278

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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