SMTL ID : 3mo0.3 (2 other biounits)

Human G9a-like (GLP, also known as EHMT1) in complex with inhibitor E11

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.78 Å

Oligo State

homo-dimer

Ligands

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

SAH.1: 13 residues within 4Å: Chain A: M.155, G.156, W.157, S.191, Y.192, R.216, N.219, H.220, Y.261, F.265, F.273, C.275, R.276 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:W.157, A:W.157, A:S.191, A:S.191, A:Y.192, A:Y.192, A:H.220, A:H.220, A:Y.261, A:R.276 SAH.11: 15 residues within 4Å: Chain B: M.155, G.156, W.157, S.191, Y.192, R.216, N.219, H.220, Y.261, F.265, F.273, S.274, C.275, R.276, C.277 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:W.157, B:W.157, B:Y.192, B:Y.192, B:H.220, B:H.220, B:R.276, B:C.277

3 x E11: N~4~-(1-benzylpiperidin-4-yl)-N~2~-[3-(dimethylamino)propyl]-6,7-dimethoxyquinazoline-2,4-diamine(Non-covalent)

E11.2: 14 residues within 4Å: Chain A: D.181, S.182, A.184, D.185, R.187, E.188, D.190, L.193, D.195, R.264, F.265, I.268, K.269 Ligands: E11.8 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:E.188, A:L.193, A:L.193, A:I.268 Hydrogen bonds: A:D.190, A:D.190 Salt bridges: A:D.181, A:D.185 E11.8: 14 residues within 4Å: Chain A: D.181, A.184, D.185, R.187, E.188, D.190, L.193, D.195, C.205, R.264, F.265, I.268, K.269 Ligands: E11.2 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:E.188, A:L.193, A:I.268 Hydrogen bonds: A:D.190, A:D.190 Salt bridges: A:D.181 E11.12: 9 residues within 4Å: Chain B: D.181, A.184, D.185, R.187, D.190, L.193, D.195, F.265, I.268 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:D.190, B:L.193, B:L.193, B:I.268 Hydrogen bonds: B:D.190, B:D.190, B:D.195 Salt bridges: B:D.185, B:D.185

10 x ZN: ZINC ION(Non-covalent)

ZN.3: 7 residues within 4Å: Chain A: C.81, C.94, C.124, C.128, C.130 Ligands: ZN.4, ZN.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.81, A:C.94, A:C.124, A:C.128 ZN.4: 7 residues within 4Å: Chain A: C.81, C.87, C.124, C.130, C.134 Ligands: ZN.3, ZN.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.87, A:C.124, A:C.130, A:C.134 ZN.5: 7 residues within 4Å: Chain A: C.81, C.83, C.87, C.92, C.124 Ligands: ZN.3, ZN.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.81, A:C.83, A:C.87, A:C.92 ZN.6: 4 residues within 4Å: Chain A: C.222, C.275, C.277, C.282 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.222, A:C.275, A:C.282 ZN.7: 4 residues within 4Å: Chain A: H.77, H.126, H.235 Chain B: C.64 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Metal complexes: A:H.77, A:H.126, A:H.235, B:C.64 ZN.13: 6 residues within 4Å: Chain B: C.81, C.94, C.124, C.128 Ligands: ZN.14, ZN.15 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.81, B:C.94, B:C.124, B:C.128 ZN.14: 6 residues within 4Å: Chain B: C.87, C.124, C.130, C.134 Ligands: ZN.13, ZN.15 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.87, B:C.124, B:C.130, B:C.134 ZN.15: 7 residues within 4Å: Chain B: C.81, C.83, C.87, C.92, C.124 Ligands: ZN.13, ZN.14 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.81, B:C.83, B:C.87, B:C.92 ZN.16: 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 ZN.17: 4 residues within 4Å: Chain A: C.64 Chain B: H.77, H.126, H.235 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Metal complexes: B:H.77, B:H.126, B:H.235, A:C.64

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.9: 5 residues within 4Å: Chain B: D.32, G.36, E.38, I.40, P.41 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.38 EDO.10: 5 residues within 4Å: Chain B: I.33, R.35, Y.57, K.58, Y.59 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.35, B:Y.59

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
A

B
B

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

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