SMTL ID : 7bhu.1

Crystal structure of MAT2a with elaborated fragment 26 bound in the allosteric site

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.15 Å

Oligo State

homo-dimer

Ligands

2 x TOW: 7-chloranyl-4-(dimethylamino)-1-(2-hydroxyethyl)quinazolin-2-one(Non-covalent)

TOW.1: 18 residues within 4Å: Chain A: F.20, F.22, Q.192, V.197, G.275, W.276, G.277, R.315, Y.337 Chain B: A.278, L.317, Q.319, S.333, I.334, F.335, E.344 Ligands: EDO.3, EDO.6 10 PLIP interactions: 7 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:F.20, B:L.317, B:F.335 Hydrogen bonds: A:G.275, A:R.315, A:R.315 Water bridges: A:G.277 pi-Stacking: A:F.22, A:W.276, B:F.335 TOW.4: 18 residues within 4Å: Chain A: A.278, L.317, Q.319, S.333, I.334, F.335, E.344 Chain B: F.20, F.22, Q.192, V.197, G.275, W.276, G.277, R.315, Y.337 Ligands: EDO.3, EDO.6 10 PLIP interactions: 3 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:L.317, A:F.335, B:F.20 pi-Stacking: A:F.335, B:F.22, B:W.276 Hydrogen bonds: B:G.275, B:R.315, B:R.315 Water bridges: B:G.277

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

SAM.2: 18 residues within 4Å: Chain A: H.31, P.32, D.181, K.183, S.208, S.249, R.251, F.252, 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: 11 interactions with chain A, 9 interactions with chain B Hydrogen bonds: A:D.181, A:S.249, A:R.251, A:D.260, A:D.260, B:E.72, B:E.72, B:Q.115 Water bridges: A:S.208, A:S.249, A:A.261, B:I.119, B:I.119, B:K.291, B:K.291 Salt bridges: A:D.260, B:D.136, B:K.291 pi-Stacking: A:F.252, A:F.252 SAM.5: 18 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, D.260 20 PLIP interactions: 9 interactions with chain A, 11 interactions with chain B Hydrogen bonds: A:E.72, A:E.72, A:Q.115, B:D.181, B:S.249, B:R.251, B:D.260, B:D.260 Water bridges: A:I.119, A:I.119, A:K.291, A:K.291, B:S.208, B:S.249, B:A.261 Salt bridges: A:D.136, A:K.291, B:D.260 pi-Stacking: B:F.252, B:F.252

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

EDO.3: 7 residues within 4Å: Chain A: G.277, Y.337 Chain B: G.277, Y.337 Ligands: TOW.1, TOW.4, EDO.6 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:G.277, A:Y.337, A:Y.337, B:G.277, B:Y.337, B:Y.337 EDO.6: 7 residues within 4Å: Chain A: G.277, Y.337 Chain B: G.277, Y.337 Ligands: TOW.1, EDO.3, TOW.4 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:G.277, A:Y.337, A:Y.337, B:G.277, B:Y.337, B:Y.337

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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