SMTL ID : 5tuy.1

Structure of human G9a SET-domain (EHMT2) in complex with inhibitor MS0124

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: C.60, C.97, C.103, C.107 Ligands: ZN.2, ZN.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.60, A:C.97, A:C.103, A:C.107 ZN.2: 7 residues within 4Å: Chain A: C.54, C.67, C.97, C.101, C.103 Ligands: ZN.1, ZN.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.54, A:C.67, A:C.97, A:C.101 ZN.3: 7 residues within 4Å: Chain A: C.54, C.56, C.60, C.65, C.97 Ligands: ZN.1, ZN.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.54, A:C.56, A:C.60, A:C.65 ZN.4: 4 residues within 4Å: Chain A: C.195, C.248, C.250, C.255 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.195, A:C.248, A:C.250, A:C.255 ZN.7: 6 residues within 4Å: Chain B: C.60, C.97, C.103, C.107 Ligands: ZN.8, ZN.9 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.60, B:C.97, B:C.103, B:C.107 ZN.8: 6 residues within 4Å: Chain B: C.54, C.67, C.97, C.101 Ligands: ZN.7, ZN.9 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.54, B:C.67, B:C.97, B:C.101 ZN.9: 6 residues within 4Å: Chain B: C.54, C.56, C.60, C.65 Ligands: ZN.7, ZN.8 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.54, B:C.56, B:C.60, B:C.65 ZN.10: 4 residues within 4Å: Chain B: C.195, C.248, C.250, C.255 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.195, B:C.248, B:C.250, B:C.255

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

SAM.5: 16 residues within 4Å: Chain A: M.128, G.129, W.130, S.164, Y.165, R.189, F.190, I.191, N.192, H.193, Y.234, F.238, F.246, T.247, C.248, Q.249 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:W.130, A:S.164, A:Y.165, A:N.192, A:H.193, A:H.193, A:Q.249 Water bridges: A:R.124 SAM.11: 16 residues within 4Å: Chain B: M.128, G.129, W.130, S.164, Y.165, R.189, F.190, I.191, N.192, H.193, Y.234, F.238, F.246, T.247, C.248, Q.249 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:W.130, B:S.164, B:Y.165, B:N.192, B:N.192, B:H.193, B:H.193, B:Y.234, B:Q.249 Water bridges: B:S.164

2 x 7L6: 6,7-dimethoxy-N-(1-methylpiperidin-4-yl)-2-(morpholin-4-yl)quinazolin-4-amine(Non-covalent)

7L6.6: 11 residues within 4Å: Chain A: D.154, A.157, D.158, R.160, D.163, L.166, D.168, C.178, R.237, F.238, K.242 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:D.163, A:L.166, A:L.166, A:R.237 Hydrogen bonds: A:D.163, A:D.163 Salt bridges: A:D.158, A:E.161 7L6.12: 11 residues within 4Å: Chain B: D.154, A.157, D.158, R.160, D.163, L.166, D.168, C.178, F.238, I.241, K.242 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.166 Hydrogen bonds: B:D.163 Salt bridges: B:D.163

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xiong, Y. et al., Discovery of Potent and Selective Inhibitors for G9a-Like Protein (GLP) Lysine Methyltransferase. J. Med. Chem. (2017)

Release Date

2017-02-22

Peptides

Histone-lysine N-methyltransferase EHMT2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Histone-lysine N-methyltransferase EHMT2