SMTL ID : 8p1v.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.54 Å

Oligo State

homo-dimer

Ligands

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

SAM.1: 20 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 Ligands: CL.3 21 PLIP interactions: 12 interactions with chain A, 9 interactions with chain B Hydrogen bonds: A:H.46, A:S.264, A:R.266, A:D.275, A:D.275, B:E.87, B:E.87, B:Q.130 Water bridges: A:D.48, A:S.223, A:S.264, A:A.276, B:I.134, B:I.134, 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: 20 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 Ligands: CL.13 21 PLIP interactions: 12 interactions with chain B, 9 interactions with chain A Hydrogen bonds: B:H.46, B:S.264, B:R.266, B:D.275, B:D.275, A:E.87, A:E.87, A:Q.130 Water bridges: B:D.48, B:S.223, B:S.264, B:A.276, A:I.134, A:I.134, 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 WIV: 6-cyclopropyl-~{N}-(2-methylindazol-5-yl)-1-propan-2-yl-pyrazolo[3,4-b]pyridine-4-carboxamide(Non-covalent)

WIV.2: 20 residues within 4Å: Chain A: F.35, F.37, Q.207, D.208, R.209, G.210, A.211, V.212, G.290, W.291, G.292, R.330, Y.352 Chain B: G.292, A.293, L.332, Q.334, S.348, F.350 Ligands: WIV.12 18 PLIP interactions: 5 interactions with chain B, 13 interactions with chain A Hydrophobic interactions: B:A.293, B:L.332, B:Q.334, B:F.350, A:F.35, A:F.37, A:F.37, A:Q.207, A:Q.207, A:V.212 pi-Stacking: 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 WIV.12: 20 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, V.212, G.290, W.291, G.292, R.330, Y.352 Ligands: WIV.2 18 PLIP interactions: 13 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:F.35, B:F.37, B:F.37, B:Q.207, B:Q.207, B:V.212, A:A.293, A:L.332, A:Q.334, 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

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

CL.3: 6 residues within 4Å: Chain A: H.46, K.198, K.282 Chain B: D.151 Ligands: SAM.1, CL.4 Ligand excluded by PLIP CL.4: 2 residues within 4Å: Chain B: K.302 Ligands: CL.3 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain A: L.327, S.355, Q.356 Ligand excluded by PLIP CL.6: 1 residues within 4Å: Chain A: A.179 Ligand excluded by PLIP CL.13: 6 residues within 4Å: Chain A: D.151 Chain B: H.46, K.198, K.282 Ligands: SAM.11, CL.14 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain A: K.302 Ligands: CL.13 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain B: L.327, S.355, Q.356 Ligand excluded by PLIP CL.16: 1 residues within 4Å: Chain B: A.179 Ligand excluded by PLIP

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

EDO.7: 1 residues within 4Å: Chain B: H.260 2 PLIP interactions: 2 interactions with chain B Water bridges: B:H.260, B:H.260 EDO.8: 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.146 Water bridges: A:R.142 EDO.9: 6 residues within 4Å: Chain A: S.348, I.349, E.359, R.360 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.10: 7 residues within 4Å: Chain A: W.317, N.369, F.370, D.371, V.376, D.380, K.408 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.371 Water bridges: A:R.379 EDO.17: 1 residues within 4Å: Chain A: H.260 2 PLIP interactions: 2 interactions with chain A Water bridges: A:H.260, A:H.260 EDO.18: 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.146 Water bridges: B:R.142 EDO.19: 6 residues within 4Å: Chain A: T.34, F.35 Chain B: S.348, I.349, E.359, R.360 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:I.349, B:I.349 Water bridges: A:L.36 EDO.20: 7 residues within 4Å: Chain B: W.317, N.369, F.370, D.371, V.376, D.380, K.408 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.371 Water bridges: B:R.379

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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