SMTL ID : 7rwg.1

Crystal structure of human methionine adenosyltransferase 2A (MAT2A) in complex with SAM and allosteric inhibitor AGI-43192

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 0.97 Å

Oligo State

homo-dimer

Ligands

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

SAM.1: 24 residues within 4Å: Chain A: H.30, P.31, D.180, K.182, S.207, S.248, R.250, F.251, I.253, G.254, 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.2 19 PLIP interactions: 8 interactions with chain A, 11 interactions with chain B Hydrogen bonds: A:R.250, A:D.259, B:E.71, B:Q.114 Water bridges: A:S.207, A:S.248, A:A.260, B:I.118, B:I.118, B:G.134, B:K.290, B:K.290, B:K.290, B:K.290 Salt bridges: A:D.259, B:D.135, B:K.290 pi-Stacking: A:F.251, A:F.251 SAM.10: 24 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, I.253, G.254, G.258, D.259 Ligands: CL.11 19 PLIP interactions: 8 interactions with chain B, 11 interactions with chain A Hydrogen bonds: B:R.250, B:D.259, A:E.71, A:Q.114 Water bridges: B:S.207, B:S.248, B:A.260, A:I.118, A:I.118, A:G.134, A:K.290, A:K.290, A:K.290, A:K.290 Salt bridges: B:D.259, A:D.135, A:K.290 pi-Stacking: B:F.251, B:F.251

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

CL.2: 5 residues within 4Å: Chain A: H.30, K.182, K.266 Chain B: D.135 Ligands: SAM.1 Ligand excluded by PLIP CL.11: 5 residues within 4Å: Chain A: D.135 Chain B: H.30, K.182, K.266 Ligands: SAM.10 Ligand excluded by PLIP

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

EDO.3: 6 residues within 4Å: Chain A: K.229, A.230, V.231, V.232, P.233, A.234 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.230 Water bridges: A:A.234 EDO.4: 9 residues within 4Å: Chain A: H.210, E.212, V.214, L.216, M.219, G.249, R.250, F.251, V.252 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.210, A:R.250 Water bridges: A:H.210, A:L.216 EDO.5: 5 residues within 4Å: Chain A: Q.81, K.82, R.85, E.86, Y.102 3 PLIP interactions: 3 interactions with chain A Water bridges: A:Q.81, A:K.82, A:R.85 EDO.6: 6 residues within 4Å: Chain A: V.156, H.159, K.160, A.163, Y.378, R.383 No protein-ligand interaction detected (PLIP) EDO.7: 3 residues within 4Å: Chain A: L.394, K.395, Y.396 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.396, A:Y.396, A:Y.396 EDO.12: 6 residues within 4Å: Chain B: K.229, A.230, V.231, V.232, P.233, A.234 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.230 Water bridges: B:A.234 EDO.13: 9 residues within 4Å: Chain B: H.210, E.212, V.214, L.216, M.219, G.249, R.250, F.251, V.252 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.210, B:R.250 Water bridges: B:H.210, B:L.216 EDO.14: 5 residues within 4Å: Chain B: Q.81, K.82, R.85, E.86, Y.102 3 PLIP interactions: 3 interactions with chain B Water bridges: B:Q.81, B:K.82, B:R.85 EDO.15: 6 residues within 4Å: Chain B: V.156, H.159, K.160, A.163, Y.378, R.383 No protein-ligand interaction detected (PLIP) EDO.16: 3 residues within 4Å: Chain B: L.394, K.395, Y.396 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.396, B:Y.396, B:Y.396

2 x 7UN: (8R)-8-(4-chlorophenyl)-6-(2-methyl-2H-indazol-5-yl)-2-[(2,2,2-trifluoroethyl)amino]-5,8-dihydropyrido[4,3-d]pyrimidin-7(6H)-one(Non-covalent)

7UN.8: 22 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 20 PLIP interactions: 13 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:F.19, 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, B:S.332 pi-Stacking: A:F.19, B:F.334 Halogen bonds: A:G.274, B:S.332 Water bridges: B:I.333 7UN.17: 22 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 20 PLIP interactions: 7 interactions with chain A, 13 interactions with chain B Hydrophobic interactions: A:L.316, A:F.334, B:F.19, B:F.21, B:Q.191, B:Q.191, B:V.196, B:W.275, B:W.275 Hydrogen bonds: A:S.332, A:S.332, B:D.192, B:G.194, B:R.314, B:R.314 Water bridges: A:I.333 pi-Stacking: A:F.334, B:F.19 Halogen bonds: A:S.332, B:G.274

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 6 residues within 4Å: Chain A: A.41, V.83, E.86, A.87, H.90, Q.373 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.90, A:Q.373 Water bridges: A:E.86, A:Q.373 GOL.18: 6 residues within 4Å: Chain B: A.41, V.83, E.86, A.87, H.90, Q.373 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.90, B:Q.373 Water bridges: B:E.86, B:Q.373

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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