SMTL ID : 8p4h.1 (1 other biounit)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.71 Å

Oligo State

homo-dimer

Ligands

2 x UM6: 7-chloranyl-4-[(3R)-3-fluoranylpyrrolidin-1-yl]-1-phenyl-quinazolin-2-one(Non-covalent)

UM6.1: 18 residues within 4Å: Chain A: F.35, F.37, Q.207, V.212, G.290, W.291, G.292, R.330, Y.352 Chain B: G.292, A.293, L.332, Q.334, S.348, I.349, F.350, E.359 Ligands: UM6.8 10 PLIP interactions: 4 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:A.293, B:L.332, B:F.350, B:F.350, A:F.35, A:F.37 Hydrogen bonds: A:R.330, A:R.330 pi-Stacking: A:F.37, A:W.291 UM6.8: 18 residues within 4Å: Chain A: G.292, A.293, L.332, Q.334, S.348, I.349, F.350, E.359 Chain B: F.35, F.37, Q.207, V.212, G.290, W.291, G.292, R.330, Y.352 Ligands: UM6.1 10 PLIP interactions: 6 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:F.35, B:F.37, A:A.293, A:L.332, A:F.350 Hydrogen bonds: B:R.330, B:R.330 pi-Stacking: B:F.37, B:W.291, A:F.350

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain A: W.317, N.369, F.370, D.371, V.376, D.380, K.408 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.371, A:K.408 Water bridges: A:D.371, A:V.376 GOL.3: 7 residues within 4Å: Chain A: T.163, E.165, V.172, L.173, K.176, V.247, P.249 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.164, A:K.176, A:V.247 GOL.4: 8 residues within 4Å: Chain A: E.87, E.128, Q.129, S.131 Chain B: K.78, I.269, Q.273, G.274 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.78, B:K.78 Water bridges: B:Q.273 GOL.5: 1 residues within 4Å: Chain A: D.256 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.256, A:D.256 GOL.10: 6 residues within 4Å: Chain B: T.163, E.165, V.172, L.173, K.176, P.249 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.165 Water bridges: B:E.164

1 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 3 residues within 4Å: Chain A: E.74 Chain B: D.275, A.276 6 PLIP interactions: 2 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.275, B:A.276, H2O.1, H2O.12, H2O.14, H2O.20

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

SAM.7: 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.264, R.266, F.267, I.269, D.275 Ligands: CL.9 18 PLIP interactions: 11 interactions with chain B, 7 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:E.87, A:Q.130 Water bridges: B:S.223, B:S.264, B:A.276, 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

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

CL.9: 5 residues within 4Å: Chain A: D.151 Chain B: H.46, K.198, K.282 Ligands: SAM.7 Ligand excluded by PLIP

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
A

B
B

S-adenosylmethionine synthase isoform type-2

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