SMTL ID : 7bhx.1

Crystal structure of MAT2a bound to allosteric inhibitor (compound 31)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.08 Å

Oligo State

homo-dimer

Ligands

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.1: 5 residues within 4Å: Chain A: K.230, A.231, V.232, V.233, P.234 No protein-ligand interaction detected (PLIP) DMS.5: 5 residues within 4Å: Chain B: K.230, A.231, V.232, V.233, P.234 No protein-ligand interaction detected (PLIP)

2 x TO5: 7-chloranyl-4-(dimethylamino)-1-pyridin-3-yl-quinazolin-2-one(Non-covalent)

TO5.2: 17 residues within 4Å: Chain A: G.277, A.278, L.317, Q.319, S.333, I.334, F.335 Chain B: F.20, F.22, Q.192, V.197, G.275, W.276, G.277, R.315, Y.337 Ligands: TO5.6 12 PLIP interactions: 8 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:F.20, B:F.22, A:A.278, A:L.317, A:F.335 Hydrogen bonds: B:R.315, B:R.315 Water bridges: B:G.277, B:Y.337 pi-Stacking: B:F.22, B:W.276, A:F.335 TO5.6: 17 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: G.277, A.278, L.317, Q.319, S.333, I.334, F.335 Ligands: TO5.2 12 PLIP interactions: 8 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:F.20, A:F.22, B:A.278, B:L.317, B:F.335 Hydrogen bonds: A:R.315, A:R.315 Water bridges: A:G.277, A:Y.337 pi-Stacking: A:F.22, A:W.276, B:F.335

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

SAM.3: 20 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 Ligands: CL.4 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.7: 20 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 Ligands: CL.8 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 CL: CHLORIDE ION(Non-functional Binders)

CL.4: 5 residues within 4Å: Chain A: H.31, K.183, K.267 Chain B: D.136 Ligands: SAM.3 Ligand excluded by PLIP CL.8: 5 residues within 4Å: Chain A: D.136 Chain B: H.31, K.183, K.267 Ligands: SAM.7 Ligand excluded by PLIP

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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