SMTL ID : 7kda.1

Crystal structure of human methionine adenosyltransferase 2A (MAT2A) in complex with SAM and allosteric inhibitor compound 34

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.24 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 18 PLIP interactions: 10 interactions with chain B, 8 interactions with chain A Hydrogen bonds: B:E.71, B:Q.114, 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.6: 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.7 18 PLIP interactions: 10 interactions with chain A, 8 interactions with chain B Hydrogen bonds: A:E.71, A:Q.114, 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 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.7: 5 residues within 4Å: Chain A: D.135 Chain B: H.30, K.182, K.266 Ligands: SAM.6 Ligand excluded by PLIP

2 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.3: 6 residues within 4Å: Chain A: A.41, V.83, E.86, A.87, H.90, Q.373 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.86, A:Q.373, A:Q.373 Water bridges: A:A.87, A:Q.373 TRS.8: 6 residues within 4Å: Chain B: A.41, V.83, E.86, A.87, H.90, Q.373 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.86, B:Q.373, B:Q.373 Water bridges: B:A.87, B:Q.373

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: K.229, A.230, V.231, V.232, P.233, A.234 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.229, A:A.230, A:V.231 Water bridges: A:A.234, A:A.234 GOL.9: 6 residues within 4Å: Chain B: K.229, A.230, V.231, V.232, P.233, A.234 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.229, B:A.230, B:V.231 Water bridges: B:A.234, B:A.234

2 x WBM: 2,3-diphenyl-5-[(1H-pyrazol-3-yl)amino]pyrazolo[1,5-a]pyrimidin-7(4H)-one(Non-covalent)

WBM.5: 21 residues within 4Å: Chain A: G.17, T.18, F.19, L.20, F.21, Q.191, 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: WBM.10 16 PLIP interactions: 8 interactions with chain A, 8 interactions with chain B Hydrophobic interactions: A:F.19, A:F.19, A:F.21, A:W.275, B:A.277, B:L.316, B:L.316, B:F.334 Hydrogen bonds: A:Q.191, A:R.314, A:R.314, B:I.333 pi-Stacking: A:F.21, B:F.334, B:F.334 Water bridges: B:I.333 WBM.10: 21 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: G.17, T.18, F.19, L.20, F.21, Q.191, G.274, W.275, G.276, R.314, Y.336 Ligands: WBM.5 16 PLIP interactions: 8 interactions with chain B, 8 interactions with chain A Hydrophobic interactions: B:F.19, B:F.19, B:F.21, B:W.275, A:A.277, A:L.316, A:L.316, A:F.334 Hydrogen bonds: B:Q.191, B:R.314, B:R.314, A:I.333 pi-Stacking: B:F.21, A:F.334, A:F.334 Water bridges: A:I.333

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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