SMTL ID : 7kdb.1

Crystal structure of human methionine adenosyltransferase 2A (MAT2A) in complex with SAM and allosteric inhibitor compound 35

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.24 Å

Oligo State

homo-dimer

Ligands

2 x WBS: 6-(4-hydroxyphenyl)-2,3-diphenyl-5-[(1H-pyrazol-3-yl)amino]pyrazolo[1,5-a]pyrimidin-7(4H)-one(Non-covalent)

WBS.1: 28 residues within 4Å: Chain A: G.17, T.18, 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, V.317, Q.318, S.332, I.333, F.334, E.343 Ligands: EDO.8, WBS.10 19 PLIP interactions: 11 interactions with chain A, 8 interactions with chain B Hydrophobic interactions: A:F.19, A:F.19, A:F.21, A:Q.191, A:Q.191, A:W.275, B:A.277, B:L.316, B:L.316, B:F.334 Hydrogen bonds: A:Q.191, A:R.193, A:G.194, A:R.314, A:R.314, B:I.333 Water bridges: B:I.333 pi-Stacking: B:F.334, B:F.334 WBS.10: 28 residues within 4Å: Chain A: F.140, G.276, A.277, L.316, V.317, Q.318, S.332, I.333, F.334, E.343 Chain B: G.17, T.18, 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: WBS.1, EDO.17 19 PLIP interactions: 8 interactions with chain A, 11 interactions with chain B Hydrophobic interactions: A:A.277, A:L.316, A:L.316, A:F.334, B:F.19, B:F.19, B:F.21, B:Q.191, B:Q.191, B:W.275 Hydrogen bonds: A:I.333, B:Q.191, B:R.193, B:G.194, B:R.314, B:R.314 Water bridges: A:I.333 pi-Stacking: A:F.334, A:F.334

4 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.9 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain A: S.97, D.211, E.212, V.252 Ligand excluded by PLIP CL.11: 5 residues within 4Å: Chain A: D.135 Chain B: H.30, K.182, K.266 Ligands: SAM.18 Ligand excluded by PLIP CL.16: 4 residues within 4Å: Chain B: S.97, D.211, E.212, V.252 Ligand excluded by PLIP

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

TRS.3: 4 residues within 4Å: Chain A: E.86, A.87, H.90, Q.373 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.86, A:Q.373 Water bridges: A:A.87, A:Q.373, A:Q.373 TRS.12: 4 residues within 4Å: Chain B: E.86, A.87, H.90, Q.373 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.86, B:Q.373 Water bridges: B:A.87, B:Q.373, B:Q.373

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

EDO.4: 8 residues within 4Å: Chain A: G.92, Y.93, D.94, K.98, R.169, L.177, R.178, P.179 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.92, A:K.98, A:R.169, A:L.177 Water bridges: A:R.178 EDO.5: 6 residues within 4Å: Chain A: R.220, Y.243, H.244, L.245, P.247 Chain B: V.325 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.244, A:L.245 EDO.8: 8 residues within 4Å: Chain A: G.194, R.314, F.334, Y.336, G.337 Chain B: F.334 Ligands: WBS.1, EDO.17 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.336 EDO.13: 8 residues within 4Å: Chain B: G.92, Y.93, D.94, K.98, R.169, L.177, R.178, P.179 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.92, B:K.98, B:R.169, B:L.177 Water bridges: B:R.178 EDO.14: 6 residues within 4Å: Chain A: V.325 Chain B: R.220, Y.243, H.244, L.245, P.247 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.244, B:L.245 EDO.17: 8 residues within 4Å: Chain A: F.334 Chain B: G.194, R.314, F.334, Y.336, G.337 Ligands: EDO.8, WBS.10 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.336

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 6 residues within 4Å: Chain A: K.229, A.230, V.231, V.232, P.233, A.234 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.230, A:V.231, A:A.234 GOL.15: 6 residues within 4Å: Chain B: K.229, A.230, V.231, V.232, P.233, A.234 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.230, B:V.231, B:A.234

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

SAM.9: 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 20 PLIP interactions: 10 interactions with chain A, 10 interactions with chain B Hydrogen bonds: A:D.180, A:S.248, 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: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.18: 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 20 PLIP interactions: 10 interactions with chain A, 10 interactions with chain B Hydrogen bonds: A:E.71, A:Q.114, 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

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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