SMTL ID : 4nvq.1

Human G9a in Complex with Inhibitor A-366

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.03 Å

Oligo State

homo-dimer

Ligands

2 x 2OD: 5'-methoxy-6'-[3-(pyrrolidin-1-yl)propoxy]spiro[cyclobutane-1,3'-indol]-2'-amine(Non-covalent)

2OD.1: 16 residues within 4Å: Chain A: Y.159, D.166, A.169, D.170, D.175, S.176, L.178, F.179, D.180, C.190, F.244, Y.246, R.249, F.250, I.253, K.254 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.159, A:L.178, A:L.178, A:F.179, A:F.244, A:F.250, A:I.253 Hydrogen bonds: A:D.170 Water bridges: A:L.178 pi-Cation interactions: A:Y.246, A:R.249 2OD.8: 15 residues within 4Å: Chain B: Y.159, D.166, A.169, D.170, D.175, S.176, L.178, F.179, D.180, F.244, Y.246, R.249, F.250, I.253, K.254 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:Y.159, B:L.178, B:L.178, B:F.179, B:F.244 Hydrogen bonds: B:D.170 Water bridges: B:L.178 pi-Cation interactions: B:Y.246, B:R.249

2 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.2: 16 residues within 4Å: Chain A: M.140, G.141, W.142, S.176, Y.177, R.201, F.202, I.203, N.204, H.205, Y.246, F.250, F.258, T.259, C.260, Q.261 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:M.140, A:W.142, A:W.142, A:N.204, A:H.205, A:H.205, A:Q.261 SAH.7: 16 residues within 4Å: Chain B: M.140, G.141, W.142, S.176, Y.177, R.201, F.202, I.203, N.204, H.205, Y.246, F.250, F.258, T.259, C.260, Q.261 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:W.142, B:W.142, B:S.176, B:Y.177, B:Y.177, B:N.204, B:H.205, B:H.205, B:Q.261

8 x ZN: ZINC ION(Non-covalent)

ZN.3: 6 residues within 4Å: Chain A: C.66, C.79, C.109, C.113 Ligands: ZN.4, ZN.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.66, A:C.79, A:C.109, A:C.113 ZN.4: 7 residues within 4Å: Chain A: C.66, C.68, C.72, C.77, C.109 Ligands: ZN.3, ZN.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.66, A:C.68, A:C.72, A:C.77 ZN.5: 6 residues within 4Å: Chain A: C.72, C.109, C.115, C.119 Ligands: ZN.3, ZN.4 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.72, A:C.109, A:C.115, A:C.119, H2O.5 ZN.6: 4 residues within 4Å: Chain A: C.207, C.260, C.262, C.267 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.207, A:C.260, A:C.262, A:C.267 ZN.9: 6 residues within 4Å: Chain B: C.72, C.109, C.115, C.119 Ligands: ZN.10, ZN.11 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.72, B:C.109, B:C.115, B:C.119 ZN.10: 7 residues within 4Å: Chain B: C.66, C.68, C.72, C.77, C.109 Ligands: ZN.9, ZN.11 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.66, B:C.68, B:C.72, B:C.77 ZN.11: 6 residues within 4Å: Chain B: C.66, C.79, C.109, C.113 Ligands: ZN.9, ZN.10 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.66, B:C.79, B:C.109, B:C.113 ZN.12: 4 residues within 4Å: Chain B: C.207, C.260, C.262, C.267 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.207, B:C.260, B:C.262, B:C.267

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sweis, R.F. et al., Discovery and development of potent and selective inhibitors of histone methyltransferase g9a. ACS Med Chem Lett (2014)

Release Date

2014-01-15

Peptides

Histone-lysine N-methyltransferase EHMT2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Histone-lysine N-methyltransferase EHMT2