SMTL ID : 7rwh.1

Crystal structure of human methionine adenosyltransferase 2A (MAT2A) in complex with SAM and allosteric inhibitor AGI-41998

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.17 Å

Oligo State

homo-dimer

Ligands

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

SAM.1: 23 residues within 4Å: Chain A: H.30, P.31, D.180, K.182, S.207, S.248, R.250, F.251, G.258, D.259 Chain B: A.56, E.71, Q.114, S.115, D.117, I.118, Q.120, G.134, D.135, K.290, I.323 Ligands: CL.9, MG.10 19 PLIP interactions: 10 interactions with chain B, 9 interactions with chain A Hydrogen bonds: B:E.71, B:Q.114, A:S.248, A:R.250, A:D.259 Water bridges: B:I.118, B:I.118, B:K.290, B:K.290, B:K.290, B:K.290, A:S.207, A:S.248, A:A.260 Salt bridges: B:D.135, B:K.290, A:D.259 pi-Stacking: A:F.251, A:F.251 SAM.13: 23 residues within 4Å: Chain A: A.56, E.71, Q.114, S.115, D.117, I.118, Q.120, G.134, D.135, K.290, I.323 Chain B: H.30, P.31, D.180, K.182, S.207, S.248, R.250, F.251, G.258, D.259 Ligands: CL.21, MG.22 19 PLIP interactions: 10 interactions with chain A, 9 interactions with chain B Hydrogen bonds: A:E.71, A:Q.114, B:S.248, B:R.250, B:D.259 Water bridges: A:I.118, A:I.118, A:K.290, A:K.290, A:K.290, A:K.290, B:S.207, B:S.248, B:A.260 Salt bridges: A:D.135, A:K.290, B:D.259 pi-Stacking: B:F.251, B:F.251

2 x 7UI: 8-(4-bromophenyl)-6-(4-methoxyphenyl)-2-[2,2,2-tris(fluoranyl)ethylamino]pyrido[4,3-d]pyrimidin-7-ol(Non-covalent)

7UI.2: 26 residues within 4Å: Chain A: F.19, L.20, F.21, Q.191, D.192, R.193, G.194, A.195, V.196, G.274, W.275, G.276, R.314 Chain B: F.140, A.277, L.316, V.317, Q.318, S.332, I.333, F.334, E.343 Ligands: EDO.3, MG.11, MG.12, MG.24 21 PLIP interactions: 13 interactions with chain A, 8 interactions with chain B Hydrophobic interactions: A:F.21, A:Q.191, A:Q.191, A:V.196, A:W.275, A:W.275, B:L.316, B:F.334 Hydrogen bonds: A:D.192, A:G.194, A:R.314, A:R.314, B:S.332 pi-Stacking: A:F.19, A:F.19, B:F.334, B:F.334 Halogen bonds: A:G.274, B:S.332 Water bridges: B:S.332, B:S.332 7UI.14: 26 residues within 4Å: Chain A: F.140, A.277, L.316, V.317, Q.318, S.332, I.333, F.334, E.343 Chain B: F.19, L.20, F.21, Q.191, D.192, R.193, G.194, A.195, V.196, G.274, W.275, G.276, R.314 Ligands: MG.12, EDO.15, MG.23, MG.24 21 PLIP interactions: 8 interactions with chain A, 13 interactions with chain B Hydrophobic interactions: A:L.316, A:F.334, B:F.21, B:Q.191, B:Q.191, B:V.196, B:W.275, B:W.275 Hydrogen bonds: A:S.332, B:D.192, B:G.194, B:R.314, B:R.314 Water bridges: A:S.332, A:S.332 pi-Stacking: A:F.334, A:F.334, B:F.19, B:F.19 Halogen bonds: A:S.332, B:G.274

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

EDO.3: 7 residues within 4Å: Chain A: G.194, R.314, F.334, Y.336 Chain B: F.334 Ligands: 7UI.2, EDO.15 No protein-ligand interaction detected (PLIP) EDO.4: 5 residues within 4Å: Chain A: K.229, A.230, V.231, V.232, P.233 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.230 EDO.5: 5 residues within 4Å: Chain A: H.159, K.160, A.163, Y.378, R.383 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.383 EDO.6: 5 residues within 4Å: Chain A: V.83, E.86, A.87, H.90, Q.373 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.86, A:Q.373 Water bridges: A:A.87 EDO.15: 7 residues within 4Å: Chain A: F.334 Chain B: G.194, R.314, F.334, Y.336 Ligands: EDO.3, 7UI.14 No protein-ligand interaction detected (PLIP) EDO.16: 5 residues within 4Å: Chain B: K.229, A.230, V.231, V.232, P.233 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.230 EDO.17: 5 residues within 4Å: Chain B: H.159, K.160, A.163, Y.378, R.383 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.383 EDO.18: 5 residues within 4Å: Chain B: V.83, E.86, A.87, H.90, Q.373 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.86, B:Q.373 Water bridges: B:A.87

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 4 residues within 4Å: Chain A: E.112, Q.113 Chain B: T.63, Q.257 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:E.112, B:T.63, B:Q.257 GOL.19: 4 residues within 4Å: Chain A: T.63, Q.257 Chain B: E.112, Q.113 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:T.63, A:Q.257, B:E.112

2 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.8: 7 residues within 4Å: Chain A: Q.81, K.82, R.85, E.86, K.89, Y.102, K.103 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Q.81 Hydrogen bonds: A:E.86, A:K.89 1PE.20: 7 residues within 4Å: Chain B: Q.81, K.82, R.85, E.86, K.89, Y.102, K.103 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Q.81 Hydrogen bonds: B:E.86, B:K.89

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

CL.9: 5 residues within 4Å: Chain A: H.30, K.182, K.266 Chain B: D.135 Ligands: SAM.1 Ligand excluded by PLIP CL.21: 5 residues within 4Å: Chain A: D.135 Chain B: H.30, K.182, K.266 Ligands: SAM.13 Ligand excluded by PLIP

6 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.10: 4 residues within 4Å: Chain B: A.56, K.286, K.290 Ligands: SAM.1 No protein-ligand interaction detected (PLIP) MG.11: 6 residues within 4Å: Chain A: Y.142, W.275, G.276, R.314, Y.336 Ligands: 7UI.2 No protein-ligand interaction detected (PLIP) MG.12: 5 residues within 4Å: Chain A: Y.336 Chain B: Y.336 Ligands: 7UI.2, 7UI.14, MG.24 No protein-ligand interaction detected (PLIP) MG.22: 4 residues within 4Å: Chain A: A.56, K.286, K.290 Ligands: SAM.13 No protein-ligand interaction detected (PLIP) MG.23: 6 residues within 4Å: Chain B: Y.142, W.275, G.276, R.314, Y.336 Ligands: 7UI.14 No protein-ligand interaction detected (PLIP) MG.24: 5 residues within 4Å: Chain A: Y.336 Chain B: Y.336 Ligands: 7UI.2, MG.12, 7UI.14 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, M. et al., Leveraging Structure-Based Drug Design to Identify Next-Generation MAT2A Inhibitors, Including Brain-Penetrant and Peripherally Efficacious Leads. J.Med.Chem. (2022)

Release Date

2022-03-23

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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