SMTL ID : 5vsc.1

Structure of human G9a SET-domain (EHMT2) in complex with inhibitor 13

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-dimer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: C.65, C.102, C.108, C.112 Ligands: ZN.2, ZN.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.65, A:C.102, A:C.108, A:C.112 ZN.2: 6 residues within 4Å: Chain A: C.59, C.72, C.102, C.106 Ligands: ZN.1, ZN.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.59, A:C.72, A:C.102, A:C.106 ZN.3: 6 residues within 4Å: Chain A: C.59, C.61, C.65, C.70 Ligands: ZN.1, ZN.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.59, A:C.61, A:C.65, A:C.70 ZN.4: 4 residues within 4Å: Chain A: C.200, C.253, C.255, C.260 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.200, A:C.253, A:C.255, A:C.260 ZN.7: 6 residues within 4Å: Chain B: C.65, C.102, C.108, C.112 Ligands: ZN.8, ZN.9 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.65, B:C.102, B:C.108, B:C.112 ZN.8: 6 residues within 4Å: Chain B: C.59, C.72, C.102, C.106 Ligands: ZN.7, ZN.9 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.59, B:C.72, B:C.102, B:C.106 ZN.9: 6 residues within 4Å: Chain B: C.59, C.61, C.65, C.70 Ligands: ZN.7, ZN.8 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.59, B:C.61, B:C.65, B:C.70 ZN.10: 4 residues within 4Å: Chain B: C.200, C.253, C.255, C.260 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.200, B:C.253, B:C.255, B:C.260

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

SAM.5: 16 residues within 4Å: Chain A: M.133, G.134, W.135, S.169, Y.170, R.194, F.195, I.196, N.197, H.198, Y.239, F.243, F.251, T.252, C.253, Q.254 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:W.135, A:S.169, A:Y.170, A:Y.170, A:N.197, A:N.197, A:H.198, A:H.198, A:Q.254 SAM.11: 16 residues within 4Å: Chain B: M.133, G.134, W.135, S.169, Y.170, R.194, F.195, I.196, N.197, H.198, Y.239, F.243, F.251, T.252, C.253, Q.254 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:W.135, B:S.169, B:Y.170, B:Y.170, B:N.197, B:N.197, B:H.198, B:H.198, B:Y.239, B:Q.254 Water bridges: B:R.129, B:S.169

2 x 9HJ: 6,7-dimethoxy-N~2~-methyl-N~4~-(1-methylpiperidin-4-yl)-N~2~-propylquinazoline-2,4-diamine(Non-covalent)

9HJ.6: 13 residues within 4Å: Chain A: D.159, A.162, D.163, R.165, D.168, L.171, D.173, V.181, C.183, R.242, F.243, I.246, K.247 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.171, A:V.181, A:I.246 Hydrogen bonds: A:D.168, A:D.168 9HJ.12: 14 residues within 4Å: Chain B: D.159, A.162, D.163, R.165, D.168, L.171, D.173, V.181, Y.182, C.183, R.242, F.243, I.246, K.247 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:A.162, B:L.171, B:L.171, B:V.181, B:I.246 Hydrogen bonds: B:D.168 Salt bridges: B:D.163

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xiong, Y. et al., Structure-activity relationship studies of G9a-like protein (GLP) inhibitors. Bioorg. Med. Chem. (2017)

Release Date

2017-07-12

Peptides

Histone-lysine N-methyltransferase EHMT2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Histone-lysine N-methyltransferase EHMT2