SMTL ID : 7kcc.1

Crystal structure of human methionine adenosyltransferase 2A (MAT2A) in complex with SAM and allosteric inhibitor AG-270

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.32 Å

Oligo State

homo-dimer

Ligands

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

CL.1: 5 residues within 4Å: Chain A: H.30, K.182, K.266 Chain B: D.135 Ligands: SAM.7 Ligand excluded by PLIP CL.5: 6 residues within 4Å: Chain A: Y.142, W.275, G.276, R.314, Y.336 Ligands: WBG.8 Ligand excluded by PLIP CL.9: 5 residues within 4Å: Chain A: D.135 Chain B: H.30, K.182, K.266 Ligands: SAM.15 Ligand excluded by PLIP CL.13: 6 residues within 4Å: Chain B: Y.142, W.275, G.276, R.314, Y.336 Ligands: WBG.16 Ligand excluded by PLIP

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

EDO.2: 6 residues within 4Å: Chain A: K.229, A.230, V.231, V.232, P.233, A.234 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.230, A:V.232 Water bridges: A:A.234, A:A.234 EDO.3: 8 residues within 4Å: Chain A: I.253, Q.257, G.258 Chain B: E.112, Q.113, Q.114, S.115, P.116 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.113, B:Q.113, A:Q.257 Water bridges: B:E.112 EDO.4: 4 residues within 4Å: Chain A: K.393, 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.6: 9 residues within 4Å: Chain A: H.210, E.212, V.214, C.215, L.216, M.219, G.249, R.250, V.252 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.250 Water bridges: A:G.249, A:F.251 EDO.10: 6 residues within 4Å: Chain B: K.229, A.230, V.231, V.232, P.233, A.234 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.230, B:V.232 Water bridges: B:A.234, B:A.234 EDO.11: 8 residues within 4Å: Chain A: E.112, Q.113, Q.114, S.115, P.116 Chain B: I.253, Q.257, G.258 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.113, A:Q.113, B:Q.257 Water bridges: A:E.112 EDO.12: 4 residues within 4Å: Chain B: K.393, 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 EDO.14: 9 residues within 4Å: Chain B: H.210, E.212, V.214, C.215, L.216, M.219, G.249, R.250, V.252 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.250 Water bridges: B:G.249, B:F.251

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

SAM.7: 23 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, G.134, D.135, K.290, I.323 Ligands: CL.1 21 PLIP interactions: 10 interactions with chain A, 11 interactions with chain B Hydrogen bonds: A:D.180, A:S.248, A:R.250, A:D.259, B:E.71, 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.15: 23 residues within 4Å: Chain A: A.56, E.71, Q.114, S.115, D.117, I.118, 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.9 21 PLIP interactions: 11 interactions with chain A, 10 interactions with chain B Hydrogen bonds: A:E.71, 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

2 x WBG: 3-(cyclohex-1-en-1-yl)-6-(4-methoxyphenyl)-2-phenyl-5-[(pyridin-2-yl)amino]pyrazolo[1,5-a]pyrimidin-7(4H)-one(Non-covalent)

WBG.8: 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: CL.5, WBG.16 19 PLIP interactions: 7 interactions with chain B, 12 interactions with chain A Hydrophobic interactions: B:A.277, B:L.316, B:L.316, B:F.334, B:E.343, A:F.19, A:F.19, A:F.19, A:F.21, A:Q.191, A:Q.191, A:W.275 pi-Stacking: B:F.334, B:F.334 Hydrogen bonds: A:Q.191, A:R.193, A:G.194, A:R.314, A:R.314 WBG.16: 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: WBG.8, CL.13 19 PLIP interactions: 12 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:F.19, B:F.19, B:F.19, B:F.21, B:Q.191, B:Q.191, B:W.275, A:A.277, A:L.316, A:L.316, A:F.334, A:E.343 Hydrogen bonds: B:Q.191, B:R.193, B:G.194, B:R.314, B:R.314 pi-Stacking: A:F.334, A:F.334

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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