SMTL ID : 8xam.1

Co-crystal structure of compound 7 in complex with MAT2A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-dimer

Ligands

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

SAM.1: 18 residues within 4Å: Chain A: H.14, P.15, D.164, K.166, S.232, R.234, F.235, I.237, D.243 Chain B: A.40, E.55, Q.98, D.101, I.102, G.118, D.119, K.274, I.307 20 PLIP interactions: 12 interactions with chain A, 8 interactions with chain B Hydrogen bonds: A:D.164, A:S.232, A:R.234, A:D.243, A:D.243, A:D.243, B:Q.98 Water bridges: A:S.191, A:S.232, A:A.244, B:I.102, B:I.102, B:K.274, B:K.274, B:K.274 Salt bridges: A:D.243, B:D.119, B:K.274 pi-Stacking: A:F.235, A:F.235 SAM.3: 19 residues within 4Å: Chain A: A.40, E.55, Q.98, D.101, I.102, G.118, D.119, K.274, I.307 Chain B: H.14, P.15, D.164, K.166, S.191, S.232, R.234, F.235, I.237, D.243 20 PLIP interactions: 12 interactions with chain B, 8 interactions with chain A Hydrogen bonds: B:D.164, B:S.232, B:R.234, B:D.243, B:D.243, B:D.243, A:E.55, A:Q.98 Water bridges: B:S.191, B:S.232, B:A.244, A:I.102, A:I.102, A:K.274, A:K.274 Salt bridges: B:D.243, A:D.119, A:K.274 pi-Stacking: B:F.235, B:F.235

1 x XRH: 2-[3-[7-chloranyl-4-(dimethylamino)-2-oxidanylidene-quinazolin-1-yl]phenoxy]-~{N}-[3-[7-chloranyl-4-(dimethylamino)-2-oxidanylidene-quinazolin-1-yl]phenyl]ethanamide(Non-covalent)

XRH.2: 31 residues within 4Å: Chain A: F.3, F.5, Q.175, V.180, G.258, W.259, G.260, A.261, R.298, L.300, Q.302, S.316, I.317, F.318, Y.320, E.327 Chain B: F.3, F.5, Q.175, G.258, W.259, G.260, A.261, R.298, L.300, Q.302, S.316, I.317, F.318, Y.320, E.327 25 PLIP interactions: 12 interactions with chain B, 13 interactions with chain A Hydrophobic interactions: B:F.3, B:F.3, B:F.5, B:W.259, B:A.261, B:L.300, B:F.318, B:F.318, A:F.3, A:F.3, A:F.5, A:W.259, A:A.261, A:F.318 Hydrogen bonds: B:R.298, B:R.298, A:G.260, A:R.298, A:R.298, A:Y.320 Water bridges: B:Y.320, A:Y.126, A:G.260 pi-Stacking: B:F.318, A:F.318

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gao, F. et al., Discovery of novel MAT2A inhibitors by an allosteric site-compatible fragment growing approach. Bioorg.Med.Chem. (2024)

Release Date

2024-02-28

Peptides

S-adenosylmethionine synthase isoform type-2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

S-adenosylmethionine synthase isoform type-2