SMTL ID : 7bhr.1

Crystal structure of MAT2a with triazinone fragment 1 bound in the allosteric site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.08 Å

Oligo State

homo-dimer

Ligands

2 x TQE: 4-(dimethylamino)-6-ethoxy-1~{H}-1,3,5-triazin-2-one(Non-covalent)

TQE.1: 10 residues within 4Å: Chain A: F.20, F.22, Q.192, W.276, R.315, Y.337 Chain B: L.317, Q.319, S.333, F.335 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:Q.319, B:F.335 pi-Stacking: B:F.335 Hydrogen bonds: A:R.315, A:R.315 Water bridges: A:G.277 TQE.3: 10 residues within 4Å: Chain A: L.317, Q.319, S.333, F.335 Chain B: F.20, F.22, Q.192, W.276, R.315, Y.337 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:Q.319, A:F.335 pi-Stacking: A:F.335 Hydrogen bonds: B:R.315, B:R.315 Water bridges: B:G.277

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

SAM.2: 19 residues within 4Å: Chain A: H.31, P.32, D.181, K.183, S.208, S.249, R.251, F.252, I.254, D.260 Chain B: A.57, E.72, Q.115, D.118, I.119, G.135, D.136, K.291, I.324 20 PLIP interactions: 9 interactions with chain B, 11 interactions with chain A Hydrogen bonds: B:E.72, B:E.72, B:Q.115, A:D.181, A:S.249, A:R.251, A:D.260, A:D.260 Water bridges: B:I.119, B:I.119, B:K.291, B:K.291, A:S.208, A:S.249, A:A.261 Salt bridges: B:D.136, B:K.291, A:D.260 pi-Stacking: A:F.252, A:F.252 SAM.4: 19 residues within 4Å: Chain A: A.57, E.72, Q.115, D.118, I.119, G.135, D.136, K.291, I.324 Chain B: H.31, P.32, D.181, K.183, S.208, S.249, R.251, F.252, I.254, D.260 20 PLIP interactions: 11 interactions with chain B, 9 interactions with chain A Hydrogen bonds: B:D.181, B:S.249, B:R.251, B:D.260, B:D.260, A:E.72, A:E.72, A:Q.115 Water bridges: B:S.208, B:S.249, B:A.261, A:I.119, A:I.119, A:K.291, A:K.291 Salt bridges: B:D.260, A:D.136, A:K.291 pi-Stacking: B:F.252, B:F.252

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

De Fusco, C. et al., Fragment-Based Design of a Potent MAT2a Inhibitor and in Vivo Evaluation in an MTAP Null Xenograft Model. 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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