SMTL ID : 7t7l.2 (1 other biounit)

Structure of human G9a SET-domain (EHMT2) in complex with covalent inhibitor (Compound 1)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: C.70, C.107, C.113, C.117 Ligands: 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: 5 residues within 4Å: Chain A: C.64, C.77, C.107, C.111 Ligands: 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: 7 residues within 4Å: Chain A: C.64, C.66, C.70, C.75, C.107 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: G5U.6 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:W.140, A:S.174, A:Y.175, A:Y.175, A:N.202, 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: G5U.12 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:W.140, B:S.174, B:Y.175, B:Y.175, B:N.202, B:H.203, B:H.203, B:Q.259

2 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.6: 17 residues within 4Å: Chain A: Y.157, D.164, A.167, D.168, D.173, S.174, L.176, F.177, D.178, C.188, F.242, Y.244, R.247, F.248, I.251, K.252 Ligands: SAM.5 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Y.157, A:A.167, A:D.173, A:L.176, A:F.177, A:F.242, A:R.247, A:I.251 Hydrogen bonds: A:D.173, A:D.173, A:R.247 Water bridges: A:L.176 pi-Cation interactions: A:Y.244, A:R.247 G5U.12: 19 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, Y.187, C.188, F.242, Y.244, R.247, F.248, I.251, K.252 Ligands: SAM.11 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:Y.157, B:D.164, B:D.173, B:L.176, B:L.176, B:F.177, B:V.186, B:F.242 Hydrogen bonds: B:D.173, B:D.173, B:R.247, B:R.247 Water bridges: B:L.176 Salt bridges: B:D.168 pi-Cation interactions: B:Y.244, B:R.247

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 EHMT2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

Histone-lysine N-methyltransferase EHMT2

Related Entries With Identical Sequence