SMTL ID : 7kcf.1

Crystal structure of human methionine adenosyltransferase 2A (MAT2A) in complex with SAM and allosteric inhibitor AGI-24512

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.10 Å

Oligo State

homo-dimer

Ligands

2 x J4A: 6-(4-hydroxyphenyl)-5-methyl-2-phenyl-3-(piperidin-1-yl)pyrazolo[1,5-a]pyrimidin-7(4H)-one(Non-covalent)

J4A.1: 25 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, Y.336 Chain B: F.140, G.276, A.277, L.316, Q.318, S.332, I.333, F.334, E.343 Ligands: EDO.5, J4A.7 18 PLIP interactions: 12 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:F.19, A:F.21, A:Q.191, A:Q.191, A:W.275, B:A.277, B:L.316, B:Q.318, B:F.334 Hydrogen bonds: A:Q.191, A:D.192, A:R.193, A:G.194, A:R.314, A:R.314 pi-Stacking: A:F.19, B:F.334, B:F.334 J4A.7: 25 residues within 4Å: Chain A: F.140, G.276, A.277, L.316, 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, Y.336 Ligands: J4A.1, EDO.11 18 PLIP interactions: 12 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:F.19, B:F.21, B:Q.191, B:Q.191, B:W.275, A:A.277, A:L.316, A:Q.318, A:F.334 Hydrogen bonds: B:Q.191, B:D.192, B:R.193, B:G.194, B:R.314, B:R.314 pi-Stacking: B:F.19, A:F.334, A:F.334

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

SAM.2: 22 residues within 4Å: Chain A: H.30, P.31, D.180, K.182, S.207, S.248, R.250, F.251, 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 21 PLIP interactions: 10 interactions with chain B, 11 interactions with chain A Hydrogen bonds: B:E.71, B:Q.114, A:H.30, A:D.180, 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.8: 22 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.254, G.258, D.259 21 PLIP interactions: 10 interactions with chain A, 11 interactions with chain B Hydrogen bonds: A:E.71, A:Q.114, B:H.30, B:D.180, 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

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

EDO.3: 7 residues within 4Å: Chain A: E.16, G.17, T.18, Q.191 Chain B: S.342, E.343, R.344 12 PLIP interactions: 6 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:S.342, B:E.343, B:R.344, A:G.17, A:T.18 Water bridges: B:E.343, B:R.344, B:R.344, A:E.16, A:G.17, A:Q.191, A:Q.191 EDO.4: 4 residues within 4Å: Chain A: P.51, D.366, K.368, K.369 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.366 Water bridges: A:D.366 EDO.5: 7 residues within 4Å: Chain A: G.194, R.314, F.334, Y.336 Chain B: F.334 Ligands: J4A.1, EDO.11 No protein-ligand interaction detected (PLIP) EDO.9: 7 residues within 4Å: Chain A: S.342, E.343, R.344 Chain B: E.16, G.17, T.18, Q.191 12 PLIP interactions: 6 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:S.342, A:E.343, A:R.344, B:G.17, B:T.18 Water bridges: A:E.343, A:R.344, A:R.344, B:E.16, B:Q.191, B:Q.191, B:Q.191 EDO.10: 4 residues within 4Å: Chain B: P.51, D.366, K.368, K.369 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.366 Water bridges: B:D.366 EDO.11: 7 residues within 4Å: Chain A: F.334 Chain B: G.194, R.314, F.334, Y.336 Ligands: EDO.5, J4A.7 No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 4 residues within 4Å: Chain A: E.86, A.87, H.90, Q.373 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.86, A:Q.373, A:Q.373 Water bridges: A:A.87, A:H.90, A:Q.373 GOL.12: 4 residues within 4Å: Chain B: E.86, A.87, H.90, Q.373 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.86, B:Q.373, B:Q.373 Water bridges: B:A.87, B:H.90, B:Q.373

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Konteatis, Z. et al., Discovery of AG-270, a First-in-Class Oral MAT2A Inhibitor for the Treatment of Tumors with Homozygous MTAP Deletion. J.Med.Chem. (2021)

Release Date

2021-04-21

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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