SMTL ID : 7xud.1

Structure of G9a in complex with compound 26a

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-dimer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: C.64, C.77, C.107, C.111 Ligands: ZN.2, ZN.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.64, A:C.77, A:C.107, A:C.111 ZN.2: 7 residues within 4Å: Chain A: C.64, C.70, C.107, C.113, C.117 Ligands: ZN.1, ZN.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.70, A:C.107, A:C.113, A:C.117 ZN.3: 6 residues within 4Å: Chain A: C.64, C.66, C.70, C.75 Ligands: ZN.1, ZN.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.64, A:C.66, A:C.70, A:C.75 ZN.4: 4 residues within 4Å: Chain A: C.205, C.258, C.260, C.265 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.205, A:C.258, A:C.260, A:C.265 ZN.9: 6 residues within 4Å: Chain B: C.64, C.77, C.107, C.111 Ligands: ZN.10, ZN.11 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.64, B:C.77, B:C.107, B:C.111 ZN.10: 6 residues within 4Å: Chain B: C.70, C.107, C.113, C.117 Ligands: ZN.9, ZN.11 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.70, B:C.107, B:C.113, B:C.117 ZN.11: 6 residues within 4Å: Chain B: C.64, C.66, C.70, C.75 Ligands: ZN.9, ZN.10 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.64, B:C.66, B:C.70, B:C.75 ZN.12: 4 residues within 4Å: Chain B: C.205, C.258, C.260, C.265 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.205, B:C.258, B:C.260, B:C.265

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 2 residues within 4Å: Chain A: P.26, R.129 Ligand excluded by PLIP

2 x SFG: SINEFUNGIN(Non-covalent)

SFG.6: 17 residues within 4Å: Chain A: M.138, G.139, W.140, S.174, Y.175, R.199, F.200, I.201, N.202, H.203, Y.244, F.248, W.249, F.256, T.257, C.258, Q.259 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.244 Hydrogen bonds: A:W.140, A:S.174, A:Y.175, A:R.199, A:N.202, A:N.202, A:H.203, A:H.203, A:Y.244, A:Q.259 Water bridges: A:I.201 SFG.13: 17 residues within 4Å: Chain B: M.138, G.139, W.140, S.174, Y.175, R.199, F.200, I.201, N.202, H.203, Y.244, F.248, W.249, F.256, T.257, C.258, Q.259 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:W.140, B:S.174, B:Y.175, B:Y.175, B:R.199, B:N.202, B:N.202, B:H.203, B:H.203, B:Q.259 Water bridges: B:S.174, B:I.201

2 x I6Z: ~{N}-[(2~{S})-4-cyclopropyl-1-oxidanylidene-1-phenylazanyl-butan-2-yl]-3,6,6-trimethyl-4-oxidanylidene-5,7-dihydro-1~{H}-indole-2-carboxamide(Non-covalent)

I6Z.7: 15 residues within 4Å: Chain A: Y.157, D.173, S.174, L.176, F.177, D.178, D.180, P.211, R.213, F.242, D.243, Y.244, R.247, F.248, I.251 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:Y.157, A:D.173, A:F.177, A:D.180, A:F.242, A:Y.244, A:Y.244, A:F.248, A:I.251 Hydrogen bonds: A:L.176, A:D.178, A:D.178, A:Y.244, A:F.248 Water bridges: A:R.247, A:R.247 pi-Stacking: A:F.177 I6Z.14: 14 residues within 4Å: Chain B: Y.157, D.173, S.174, L.176, F.177, D.178, P.211, R.213, F.242, D.243, Y.244, R.247, F.248, I.251 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:Y.157, B:D.173, B:F.177, B:Y.244, B:Y.244, B:Y.244, B:I.251 Hydrogen bonds: B:L.176, B:D.178, B:D.178, B:Y.244, B:F.248 Water bridges: B:R.247, B:R.247 pi-Stacking: B:F.177

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

EDO.8: 5 residues within 4Å: Chain A: N.46, C.47, E.48, R.56 Chain B: R.56 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.48, A:R.56 Water bridges: A:R.56, B:R.56 EDO.16: 7 residues within 4Å: Chain B: D.32, R.134, T.135, A.136, K.137, M.138, G.139 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.135, B:G.139 EDO.17: 6 residues within 4Å: Chain B: N.46, I.54, L.161, H.218, F.223, R.225 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.46, B:F.223 Water bridges: B:N.46, B:N.46, B:R.225, B:R.225, B:R.225

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.15: 3 residues within 4Å: Chain A: E.45, L.217 Chain B: E.45 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.45 Water bridges: A:E.45

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nishigaya, Y. et al., Discovery of Novel Substrate-Competitive Lysine Methyltransferase G9a Inhibitors as Anticancer Agents. J.Med.Chem. (2023)

Release Date

2023-03-29

Peptides

Histone-lysine N-methyltransferase EHMT2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Histone-lysine N-methyltransferase EHMT2

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