SMTL ID : 8p1w.1

Crystal structure of human methionine adenosyltransferase 2A (MAT2A) in complex with allosteric compound STL232591

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.15 Å

Oligo State

homo-dimer

Ligands

2 x MTA: 5'-DEOXY-5'-METHYLTHIOADENOSINE(Non-covalent)

MTA.1: 16 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: D.133, I.134, G.150, D.151, I.339 Ligands: ABA.2 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:H.46, A:S.264, A:R.266, A:D.275 Water bridges: A:S.223, A:S.264, B:I.134, B:I.134 pi-Stacking: A:F.267, A:F.267 MTA.12: 16 residues within 4Å: Chain A: D.133, I.134, G.150, D.151, 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: ABA.13 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:H.46, B:S.264, B:R.266, B:D.275 Water bridges: B:S.223, B:S.264, A:I.134, A:I.134 pi-Stacking: B:F.267, B:F.267

2 x ABA: ALPHA-AMINOBUTYRIC ACID(Non-functional Binders)

ABA.2: 7 residues within 4Å: Chain A: D.275 Chain B: A.72, E.87, Q.130, I.134, K.306 Ligands: MTA.1 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:E.87, B:E.87, B:Q.130, A:D.275 Water bridges: B:K.306, B:K.306, A:A.276 Salt bridges: B:K.306 ABA.13: 7 residues within 4Å: Chain A: A.72, E.87, Q.130, I.134, K.306 Chain B: D.275 Ligands: MTA.12 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:E.87, A:E.87, A:Q.130, B:D.275 Water bridges: A:K.306, A:K.306, B:A.276 Salt bridges: A:K.306

2 x WK5: 8-methoxy-1-(4-methoxyphenyl)-3-methyl-2-oxidanyl-[1]benzofuro[3,2-c]pyridine(Non-covalent)

WK5.3: 14 residues within 4Å: Chain A: F.35, F.37, Q.207, G.290, W.291, G.292, R.330 Chain B: A.293, L.332, S.348, I.349, F.350, E.359 Ligands: EDO.11 14 PLIP interactions: 10 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:F.35, A:F.37, A:W.291, A:W.291, B:F.350, B:F.350 Hydrogen bonds: A:R.330, A:R.330 Water bridges: A:G.292 pi-Stacking: A:F.35, A:F.35, B:F.350, B:F.350 pi-Cation interactions: A:R.330 WK5.14: 14 residues within 4Å: Chain A: A.293, L.332, S.348, I.349, F.350, E.359 Chain B: F.35, F.37, Q.207, G.290, W.291, G.292, R.330 Ligands: EDO.22 14 PLIP interactions: 10 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:F.35, B:F.37, B:W.291, B:W.291, A:F.350, A:F.350 Hydrogen bonds: B:R.330, B:R.330 Water bridges: B:G.292 pi-Stacking: B:F.35, B:F.35, A:F.350, A:F.350 pi-Cation interactions: B:R.330

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

CL.4: 3 residues within 4Å: Chain A: E.102, A.103, Q.389 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain A: T.163, E.164, E.165 Ligand excluded by PLIP CL.6: 1 residues within 4Å: Chain A: F.370 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain B: E.102, A.103, Q.389 Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain B: T.163, E.164, E.165 Ligand excluded by PLIP CL.17: 1 residues within 4Å: Chain B: F.370 Ligand excluded by PLIP

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

EDO.7: 5 residues within 4Å: Chain A: K.245, A.246, V.247, V.248, P.249 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.246 EDO.8: 5 residues within 4Å: Chain A: H.175, K.176, A.179, Y.394, R.399 1 PLIP interactions: 1 interactions with chain A Water bridges: A:G.398 EDO.9: 3 residues within 4Å: Chain A: L.410, K.411, Y.412 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.412, A:Y.412, A:Y.412 EDO.10: 9 residues within 4Å: Chain A: M.155, F.156, T.287, A.293, H.294, G.295, F.299, A.312, F.397 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.156, A:G.295 Water bridges: A:H.294, A:G.297 EDO.11: 6 residues within 4Å: Chain A: T.34, F.35 Chain B: S.348, I.349, E.359 Ligands: WK5.3 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:I.349, B:I.349, A:T.34 Water bridges: A:L.36 EDO.18: 5 residues within 4Å: Chain B: K.245, A.246, V.247, V.248, P.249 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.246 EDO.19: 5 residues within 4Å: Chain B: H.175, K.176, A.179, Y.394, R.399 1 PLIP interactions: 1 interactions with chain B Water bridges: B:G.398 EDO.20: 3 residues within 4Å: Chain B: L.410, K.411, Y.412 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.412, B:Y.412, B:Y.412 EDO.21: 9 residues within 4Å: Chain B: M.155, F.156, T.287, A.293, H.294, G.295, F.299, A.312, F.397 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:F.156, B:G.295 Water bridges: B:H.294, B:G.297 EDO.22: 6 residues within 4Å: Chain A: S.348, I.349, E.359 Chain B: T.34, F.35 Ligands: WK5.14 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:I.349, A:I.349, B:T.34 Water bridges: B:L.36

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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