SMTL ID : 7t7m.1 (1 other biounit)

Structure of human GLP SET-domain (EHMT1) in complex with covalent inhibitor (Compound 1)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.85 Å

Oligo State

homo-dimer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 7 residues within 4Å: Chain A: C.83, C.96, C.126, C.130, C.132 Ligands: ZN.2, ZN.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.83, A:C.96, A:C.126, A:C.130 ZN.2: 6 residues within 4Å: Chain A: C.89, C.126, C.132, C.136 Ligands: ZN.1, ZN.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.89, A:C.126, A:C.132, A:C.136 ZN.3: 7 residues within 4Å: Chain A: C.83, C.85, C.89, C.94, C.126 Ligands: ZN.1, ZN.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.83, A:C.85, A:C.89, A:C.94 ZN.4: 4 residues within 4Å: Chain A: C.224, C.277, C.279, C.284 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.224, A:C.277, A:C.279, A:C.284 ZN.6: 6 residues within 4Å: Chain B: C.83, C.96, C.126, C.130 Ligands: ZN.7, ZN.8 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.83, B:C.96, B:C.126, B:C.130 ZN.7: 7 residues within 4Å: Chain B: C.83, C.89, C.126, C.132, C.136 Ligands: ZN.6, ZN.8 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.89, B:C.126, B:C.132, B:C.136 ZN.8: 6 residues within 4Å: Chain B: C.83, C.85, C.89, C.94 Ligands: ZN.6, ZN.7 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.83, B:C.85, B:C.89, B:C.94 ZN.9: 4 residues within 4Å: Chain B: C.224, C.277, C.279, C.284 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.224, B:C.277, B:C.279, B:C.284

1 x G4R: N-(6-methoxy-4-{[1-(propan-2-yl)piperidin-4-yl]amino}-7-[3-(pyrrolidin-1-yl)propoxy]quinazolin-2-yl)prop-2-enamide(Non-covalent)

G4R.5: 15 residues within 4Å: Chain A: Y.176, D.183, A.186, D.187, D.192, S.193, L.195, F.196, D.197, C.207, F.261, Y.263, R.266, F.267, I.270 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:A.186, A:L.195, A:F.261, A:Y.263, A:F.267, A:I.270 Hydrogen bonds: A:D.192, A:D.192

1 x G5U: N-(6-methoxy-4-{[1-(propan-2-yl)piperidin-4-yl]amino}-7-[3-(pyrrolidin-1-yl)propoxy]quinazolin-2-yl)propanamide(Covalent)

G5U.10: 17 residues within 4Å: Chain B: Y.176, D.183, A.186, D.187, R.189, D.192, S.193, L.195, F.196, D.197, C.207, F.261, Y.263, R.266, F.267, I.270, K.271 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:Y.176, B:D.183, B:D.192, B:L.195, B:F.196, B:F.261, B:I.270 Hydrogen bonds: B:R.266, B:R.266 Salt bridges: B:D.192 pi-Cation interactions: B:R.266

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Park, K.S. et al., Discovery of the First-in-Class G9a/GLP Covalent Inhibitors. J.Med.Chem. (2022)

Release Date

2022-07-06

Peptides

Histone-lysine N-methyltransferase EHMT1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

Histone-lysine N-methyltransferase EHMT1

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