SMTL ID : 7rw7.1

Crystal structure of human methionine adenosyltransferase 2A (MAT2A) in complex with SAM and allosteric inhibitor Compound 9

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.19 Å

Oligo State

homo-dimer

Ligands

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

SAM.1: 21 residues within 4Å: Chain A: H.30, P.31, D.180, K.182, S.207, S.248, R.250, F.251, I.253, D.259 Chain B: A.56, E.71, Q.114, D.117, I.118, G.134, D.135, K.290, I.323 Ligands: CL.2, CL.4 21 PLIP interactions: 12 interactions with chain A, 9 interactions with chain B Hydrogen bonds: A:D.180, A:S.248, A:R.250, A:D.259, A:D.259, A:D.259, B:Q.114 Water bridges: A:S.207, A:S.248, A:A.260, B:I.118, B:I.118, B:G.134, B:K.290, B:K.290, B:K.290 Salt bridges: A:D.259, B:D.135, B:K.290 pi-Stacking: A:F.251, A:F.251 SAM.10: 21 residues within 4Å: Chain A: A.56, E.71, Q.114, D.117, I.118, G.134, D.135, K.290, I.323 Chain B: H.30, P.31, D.180, K.182, S.207, S.248, R.250, F.251, I.253, D.259 Ligands: CL.11, CL.13 21 PLIP interactions: 9 interactions with chain A, 12 interactions with chain B Hydrogen bonds: A:Q.114, B:D.180, B:S.248, B:R.250, B:D.259, B:D.259, B:D.259 Water bridges: A:I.118, A:I.118, A:G.134, A:K.290, A:K.290, A:K.290, B:S.207, B:S.248, B:A.260 Salt bridges: A:D.135, A:K.290, B:D.259 pi-Stacking: B:F.251, B:F.251

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 5 residues within 4Å: Chain A: H.30, K.182, K.266 Chain B: D.135 Ligands: SAM.1 Ligand excluded by PLIP CL.4: 4 residues within 4Å: Chain B: A.56, K.286, K.290 Ligands: SAM.1 Ligand excluded by PLIP CL.11: 5 residues within 4Å: Chain A: D.135 Chain B: H.30, K.182, K.266 Ligands: SAM.10 Ligand excluded by PLIP CL.13: 4 residues within 4Å: Chain A: A.56, K.286, K.290 Ligands: SAM.10 Ligand excluded by PLIP

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

EDO.3: 5 residues within 4Å: Chain A: K.229, A.230, V.231, V.232, P.233 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.230, A:V.232 Water bridges: A:A.234 EDO.5: 7 residues within 4Å: Chain A: E.112, Q.113, Q.114, S.115, P.116 Chain B: I.253, Q.257 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.257, A:Q.114 EDO.6: 9 residues within 4Å: Chain A: F.334, Y.336 Chain B: F.334, Y.336 Ligands: EDO.7, 7UB.9, EDO.15, EDO.16, 7UB.18 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Water bridges: A:Y.336, A:Y.336, B:Y.336, B:Y.336 EDO.7: 7 residues within 4Å: Chain A: F.334, Y.336 Chain B: F.334 Ligands: EDO.6, 7UB.9, EDO.15, EDO.16 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.336 EDO.12: 5 residues within 4Å: Chain B: K.229, A.230, V.231, V.232, P.233 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.230, B:V.232 Water bridges: B:A.234 EDO.14: 7 residues within 4Å: Chain A: I.253, Q.257 Chain B: E.112, Q.113, Q.114, S.115, P.116 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.114, A:Q.257 EDO.15: 9 residues within 4Å: Chain A: F.334, Y.336 Chain B: F.334, Y.336 Ligands: EDO.6, EDO.7, 7UB.9, EDO.16, 7UB.18 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Water bridges: A:Y.336, A:Y.336, B:Y.336, B:Y.336 EDO.16: 7 residues within 4Å: Chain A: F.334 Chain B: F.334, Y.336 Ligands: EDO.6, EDO.7, EDO.15, 7UB.18 1 PLIP interactions: 1 interactions with chain B Water bridges: B:Y.336

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.8: 6 residues within 4Å: Chain A: E.15, Q.188, I.199, R.200, D.238, D.240 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.200, A:D.240, A:D.240 PEG.17: 6 residues within 4Å: Chain B: E.15, Q.188, I.199, R.200, D.238, D.240 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.200, B:D.240, B:D.240

2 x 7UB: (3'R)-2-[(cyclopropylmethyl)amino]-6-(4-methoxyphenyl)-1'-[(1H-pyrazol-5-yl)methyl]-5,6-dihydro-7H-spiro[pyrido[4,3-d]pyrimidine-8,3'-pyrrolidin]-7-one(Non-covalent)

7UB.9: 22 residues within 4Å: Chain A: F.19, L.20, F.21, Q.191, R.193, G.194, A.195, V.196, G.274, W.275, G.276, R.314 Chain B: F.140, G.276, A.277, L.316, Q.318, S.332, F.334 Ligands: EDO.6, EDO.7, EDO.15 24 PLIP interactions: 17 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:F.19, A:F.21, A:Q.191, A:Q.191, A:V.196, A:W.275, B:F.140, B:L.316, B:Q.318, B:F.334 Hydrogen bonds: A:D.192, A:G.194, A:G.276, A:R.314, A:R.314, B:S.332, B:S.332 Water bridges: A:G.276, A:Y.336, A:Y.336, A:Y.336, A:Y.336, B:G.276 pi-Stacking: A:F.19 7UB.18: 22 residues within 4Å: Chain A: F.140, G.276, A.277, L.316, Q.318, S.332, F.334 Chain B: F.19, L.20, F.21, Q.191, R.193, G.194, A.195, V.196, G.274, W.275, G.276, R.314 Ligands: EDO.6, EDO.15, EDO.16 24 PLIP interactions: 17 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:F.19, B:F.21, B:Q.191, B:Q.191, B:V.196, B:W.275, A:F.140, A:L.316, A:Q.318, A:F.334 Hydrogen bonds: B:D.192, B:G.194, B:G.276, B:R.314, B:R.314, A:S.332, A:S.332 Water bridges: B:G.276, B:Y.336, B:Y.336, B:Y.336, B:Y.336, A:G.276 pi-Stacking: B:F.19

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, M. et al., Leveraging Structure-Based Drug Design to Identify Next-Generation MAT2A Inhibitors, Including Brain-Penetrant and Peripherally Efficacious Leads. J.Med.Chem. (2022)

Release Date

2022-03-23

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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