SMTL ID : 3mo5.6 (5 other biounits)

Human G9a-like (GLP, also known as EHMT1) in complex with inhibitor E72

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.14 Å

Oligo State

homo-dimer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 7 residues within 4Å: Chain A: C.81, C.94, C.124, C.128, C.130 Ligands: ZN.2, ZN.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.81, A:C.94, A:C.124, A:C.128 ZN.2: 7 residues within 4Å: Chain A: C.81, C.87, C.124, C.130, C.134 Ligands: ZN.1, ZN.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.87, A:C.124, A:C.130, A:C.134 ZN.3: 6 residues within 4Å: Chain A: C.81, C.83, C.87, C.92 Ligands: ZN.1, ZN.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.81, A:C.83, A:C.87, A:C.92 ZN.4: 4 residues within 4Å: Chain A: C.222, C.275, C.277, C.282 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.222, A:C.275, A:C.277, A:C.282 ZN.7: 6 residues within 4Å: Chain B: C.81, C.94, C.124, C.128 Ligands: ZN.8, ZN.9 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.81, B:C.94, B:C.124, B:C.128, H2O.11 ZN.8: 6 residues within 4Å: Chain B: C.87, C.124, C.130, C.134 Ligands: ZN.7, ZN.9 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.87, B:C.124, B:C.130, B:C.134, H2O.11 ZN.9: 7 residues within 4Å: Chain B: C.81, C.83, C.87, C.92, C.124 Ligands: ZN.7, ZN.8 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.81, B:C.83, B:C.87, B:C.92 ZN.10: 4 residues within 4Å: Chain B: C.222, C.275, C.277, C.282 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.222, B:C.275, B:C.277, B:C.282

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

SAH.5: 15 residues within 4Å: Chain A: M.155, G.156, W.157, S.191, Y.192, R.216, F.217, N.219, H.220, Y.261, F.265, F.273, C.275, R.276, C.277 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:W.157, A:W.157, A:Y.192, A:N.219, A:H.220, A:H.220, A:R.276 Water bridges: A:Y.192, A:Y.192, A:R.276 SAH.11: 15 residues within 4Å: Chain B: M.155, G.156, W.157, S.191, Y.192, R.216, F.217, N.219, H.220, Y.261, F.265, F.273, C.275, R.276, C.277 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:W.157, B:W.157, B:S.191, B:Y.192, B:N.219, B:H.220, B:H.220, B:R.276

2 x E72: 7-[(5-aminopentyl)oxy]-N~4~-[1-(5-aminopentyl)piperidin-4-yl]-N~2~-[3-(dimethylamino)propyl]-6-methoxyquinazoline-2,4-diamine(Non-covalent)

E72.6: 17 residues within 4Å: Chain A: Y.174, D.181, A.184, D.185, V.186, R.187, D.190, S.191, L.193, D.195, C.205, F.259, Y.261, R.264, F.265, I.268, K.269 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.193, A:Y.261, A:F.265, A:I.268 Hydrogen bonds: A:D.181, A:D.190, A:S.191, A:D.195, A:R.264 Water bridges: A:F.265 Salt bridges: A:D.181, A:D.185, A:D.185 E72.12: 18 residues within 4Å: Chain B: Y.174, D.181, A.184, D.185, V.186, R.187, E.188, D.190, S.191, L.193, D.195, C.205, F.259, Y.261, R.264, F.265, I.268, K.269 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:D.185, B:E.188, B:L.193, B:Y.261, B:R.264, B:F.265, B:I.268 Hydrogen bonds: B:D.190, B:S.191, B:D.195 Water bridges: B:D.181 Salt bridges: B:D.181, B:D.185, B:D.185

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chang, Y. et al., Adding a lysine mimic in the design of potent inhibitors of histone lysine methyltransferases. J.Mol.Biol. (2010)

Release Date

2010-06-30

Peptides

Histone-lysine N-methyltransferase, H3 lysine-9 specific 5: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Histone-lysine N-methyltransferase, H3 lysine-9 specific 5

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