SMTL ID : 8qe2.1

Crystal structure of human MAT2a bound to S-Adenosylmethionine and Compound 21

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.11 Å

Oligo State

homo-dimer

Ligands

2 x U7X: 4-[4-[bis(fluoranyl)methoxy]phenyl]-3-cyclopropyl-6-(2-methylindazol-5-yl)-2~{H}-pyrazolo[4,3-b]pyridin-5-one(Non-covalent)

U7X.1: 21 residues within 4Å: Chain A: F.20, F.22, Q.192, D.193, R.194, G.195, A.196, V.197, G.275, W.276, G.277, R.315 Chain B: F.141, G.277, A.278, L.317, Q.319, S.333, I.334, F.335, E.344 20 PLIP interactions: 5 interactions with chain B, 15 interactions with chain A Hydrophobic interactions: B:Q.319, B:F.335, B:F.335, A:F.20, A:F.22, A:F.22, A:Q.192, A:V.197, A:W.276, A:W.276 Hydrogen bonds: B:E.344, A:D.193, A:G.195, A:G.277, A:R.315, A:R.315 Halogen bonds: B:G.277 pi-Stacking: A:F.20, A:F.20 pi-Cation interactions: A:R.315 U7X.3: 21 residues within 4Å: Chain A: F.141, G.277, A.278, L.317, Q.319, S.333, I.334, F.335, E.344 Chain B: F.20, F.22, Q.192, D.193, R.194, G.195, A.196, V.197, G.275, W.276, G.277, R.315 20 PLIP interactions: 15 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:F.20, B:F.22, B:F.22, B:Q.192, B:V.197, B:W.276, B:W.276, A:Q.319, A:F.335, A:F.335 Hydrogen bonds: B:D.193, B:G.195, B:G.277, B:R.315, B:R.315, A:E.344 pi-Stacking: B:F.20, B:F.20 pi-Cation interactions: B:R.315 Halogen bonds: A: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 22 PLIP interactions: 11 interactions with chain A, 11 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:E.72, B:Q.115 Water bridges: A:S.208, A:S.249, A:A.261, B:I.119, B:I.119, B:D.136, 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.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 22 PLIP interactions: 11 interactions with chain A, 11 interactions with chain B Hydrogen bonds: A:E.72, 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:D.136, 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Atkinson, S.J. et al., Development of a Series of Pyrrolopyridone MAT2A Inhibitors. J.Med.Chem. (2024)

Release Date

2024-03-20

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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