SMTL ID : 8p1t.1

Crystal structure of human methionine adenosyltransferase 2A (MAT2A) in complex with SAM and allosteric inhibitor Z237451470

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.44 Å

Oligo State

homo-dimer

Ligands

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

SAM.1: 19 residues within 4Å: Chain A: H.46, P.47, D.196, K.198, S.223, S.264, R.266, F.267, I.269, D.275 Chain B: A.72, E.87, Q.130, D.133, I.134, G.150, D.151, K.306, I.339 20 PLIP interactions: 11 interactions with chain A, 9 interactions with chain B Hydrogen bonds: A:D.196, A:S.264, A:R.266, A:D.275, A:D.275, B:E.87, B:Q.130 Water bridges: A:S.223, A:S.264, A:A.276, B:I.134, B:I.134, B:K.306, B:K.306, B:K.306 Salt bridges: A:D.275, B:D.151, B:K.306 pi-Stacking: A:F.267, A:F.267 SAM.11: 19 residues within 4Å: Chain A: A.72, E.87, Q.130, D.133, I.134, G.150, D.151, K.306, I.339 Chain B: H.46, P.47, D.196, K.198, S.223, S.264, R.266, F.267, I.269, D.275 20 PLIP interactions: 11 interactions with chain B, 9 interactions with chain A Hydrogen bonds: B:D.196, B:S.264, B:R.266, B:D.275, B:D.275, A:E.87, A:Q.130 Water bridges: B:S.223, B:S.264, B:A.276, A:I.134, A:I.134, A:K.306, A:K.306, A:K.306 Salt bridges: B:D.275, A:D.151, A:K.306 pi-Stacking: B:F.267, B:F.267

2 x WJL: 6-cyclopropyl-~{N}-(1~{H}-indazol-5-yl)-1-propan-2-yl-pyrazolo[3,4-b]pyridine-4-carboxamide(Non-covalent)

WJL.2: 19 residues within 4Å: Chain A: F.35, F.37, Q.207, D.208, R.209, G.210, A.211, G.290, W.291, G.292, R.330 Chain B: G.292, A.293, L.332, Q.334, S.348, F.350 Ligands: EDO.3, WJL.12 17 PLIP interactions: 11 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:F.35, A:F.37, A:Q.207, A:Q.207, B:A.293, B:L.332, B:Q.334, B:F.350, B:F.350 Hydrogen bonds: A:D.208, A:G.210, A:R.330, A:R.330 Water bridges: A:Q.207, A:G.292, A:Y.352 pi-Stacking: B:F.350 WJL.12: 19 residues within 4Å: Chain A: G.292, A.293, L.332, Q.334, S.348, F.350 Chain B: F.35, F.37, Q.207, D.208, R.209, G.210, A.211, G.290, W.291, G.292, R.330 Ligands: WJL.2, EDO.13 17 PLIP interactions: 11 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:F.35, B:F.37, B:Q.207, B:Q.207, A:A.293, A:L.332, A:Q.334, A:F.350, A:F.350 Hydrogen bonds: B:D.208, B:G.210, B:R.330, B:R.330 Water bridges: B:Q.207, B:G.292, B:Y.352 pi-Stacking: A:F.350

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

EDO.3: 6 residues within 4Å: Chain A: G.210, R.330, Y.352 Chain B: F.350 Ligands: WJL.2, EDO.13 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.352 EDO.4: 2 residues within 4Å: Chain A: I.215, K.251 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.215 EDO.5: 7 residues within 4Å: Chain A: S.348, I.349, E.359, R.360, L.363 Chain B: T.34, F.35 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:I.349, A:I.349 Water bridges: B:L.36 EDO.6: 4 residues within 4Å: Chain A: D.141, R.142, N.143, D.146 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.141, A:N.143 EDO.7: 1 residues within 4Å: Chain B: H.260 1 PLIP interactions: 1 interactions with chain B Water bridges: B:H.260 EDO.8: 7 residues within 4Å: Chain A: W.317, N.369, F.370, D.371, V.376, D.380, K.408 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.371 EDO.13: 6 residues within 4Å: Chain A: F.350 Chain B: G.210, R.330, Y.352 Ligands: EDO.3, WJL.12 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.352 EDO.14: 2 residues within 4Å: Chain B: I.215, K.251 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:I.215 EDO.15: 7 residues within 4Å: Chain A: T.34, F.35 Chain B: S.348, I.349, E.359, R.360, L.363 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Water bridges: A:L.36 Hydrogen bonds: B:I.349, B:I.349 EDO.16: 4 residues within 4Å: Chain B: D.141, R.142, N.143, D.146 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.141, B:N.143 EDO.17: 1 residues within 4Å: Chain A: H.260 1 PLIP interactions: 1 interactions with chain A Water bridges: A:H.260 EDO.18: 7 residues within 4Å: Chain B: W.317, N.369, F.370, D.371, V.376, D.380, K.408 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.371

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

CL.9: 1 residues within 4Å: Chain A: A.179 Ligand excluded by PLIP CL.19: 1 residues within 4Å: Chain B: A.179 Ligand excluded by PLIP

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

NA.10: 3 residues within 4Å: Chain A: D.275, A.276 Chain B: E.74 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.74 NA.20: 3 residues within 4Å: Chain A: E.74 Chain B: D.275, A.276 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.275

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kalliokoski, T. et al., Discovery of novel methionine adenosyltransferase 2A (MAT2A) allosteric inhibitors by structure-based virtual screening. Bioorg.Med.Chem.Lett. (2023)

Release Date

2023-08-30

Peptides

S-adenosylmethionine synthase isoform type-2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
AAA

S-adenosylmethionine synthase isoform type-2

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