SMTL ID : 7btv.1

Crystal structure of EHMT2 SET domain in complex with compound 5.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: C.70, C.107, C.113, C.117 Ligands: ZN.2, ZN.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.70, A:C.107, A:C.113, A:C.117 ZN.2: 6 residues within 4Å: Chain A: C.64, C.77, C.107, C.111 Ligands: ZN.1, ZN.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.64, A:C.77, A:C.107, A:C.111 ZN.3: 6 residues within 4Å: Chain A: C.64, C.66, C.70, C.75 Ligands: ZN.1, ZN.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.64, A:C.66, A:C.70, A:C.75 ZN.4: 4 residues within 4Å: Chain A: C.205, C.258, C.260, C.265 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.205, A:C.258, A:C.260, A:C.265 ZN.7: 6 residues within 4Å: Chain B: C.70, C.107, C.113, C.117 Ligands: ZN.8, ZN.9 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.70, B:C.107, B:C.113, B:C.117 ZN.8: 6 residues within 4Å: Chain B: C.64, C.77, C.107, C.111 Ligands: ZN.7, ZN.9 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.64, B:C.77, B:C.107, B:C.111 ZN.9: 7 residues within 4Å: Chain B: C.64, C.66, C.70, C.75, C.107 Ligands: ZN.7, ZN.8 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.64, B:C.66, B:C.70, B:C.75 ZN.10: 4 residues within 4Å: Chain B: C.205, C.258, C.260, C.265 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.205, B:C.258, B:C.260, B:C.265

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

SAM.5: 18 residues within 4Å: Chain A: M.138, G.139, W.140, S.174, Y.175, R.199, F.200, I.201, N.202, H.203, Y.244, F.248, W.249, F.256, T.257, C.258, Q.259 Ligands: N47.6 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:W.140, A:S.174, A:Y.175, A:N.202, A:H.203, A:H.203, A:Q.259 SAM.11: 17 residues within 4Å: Chain B: M.138, G.139, W.140, S.174, Y.175, R.199, F.200, I.201, N.202, H.203, Y.244, F.248, F.256, T.257, C.258, Q.259 Ligands: N47.12 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:W.140, B:Y.175, B:Y.175, B:N.202, B:N.202, B:H.203, B:H.203, B:Q.259

2 x N47: N~2~-{4-methoxy-3-[3-(pyrrolidin-1-yl)propoxy]phenyl}-N~4~,6-dimethylpyrimidine-2,4-diamine(Non-covalent)

N47.6: 18 residues within 4Å: Chain A: Y.157, D.164, A.167, D.168, D.173, S.174, L.176, F.177, D.178, V.186, C.188, F.242, Y.244, R.247, F.248, I.251, K.252 Ligands: SAM.5 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:Y.157, A:D.164, A:A.167, A:L.176, A:F.177, A:V.186, A:F.242, A:I.251 Hydrogen bonds: A:D.168, A:D.168, A:D.178 Water bridges: A:L.176, A:F.248 pi-Cation interactions: A:Y.244, A:R.247 N47.12: 18 residues within 4Å: Chain B: Y.157, D.164, A.167, D.168, D.173, S.174, L.176, F.177, D.178, V.186, C.188, F.242, Y.244, R.247, F.248, I.251, K.252 Ligands: SAM.11 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:Y.157, B:A.167, B:L.176, B:F.177, B:V.186, B:F.248, B:I.251 Hydrogen bonds: B:D.168, B:D.178 Water bridges: B:L.176, B:F.248 pi-Cation interactions: B:Y.244, B:R.247

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Katayama, K. et al., Discovery of novel histone lysine methyltransferase G9a/GLP (EHMT2/1) inhibitors: Design, synthesis, and structure-activity relationships of 2,4-diamino-6-methylpyrimidines. Bioorg.Med.Chem.Lett. (2020)

Release Date

2020-11-11

Peptides

Histone-lysine N-methyltransferase EHMT2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Histone-lysine N-methyltransferase EHMT2

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