SMTL ID : 9klc.1

G9a in complex with the S-isomer of RK-131902 (racemic compound rac-10a)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 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: 6 residues within 4Å: Chain A: 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: 7 residues within 4Å: Chain A: C.64, C.66, C.70, C.75, C.107 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.7: 6 residues within 4Å: Chain B: C.64, C.77, C.107, C.111 Ligands: ZN.8, ZN.9 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.64, B:C.77, B:C.107, B:C.111 ZN.8: 6 residues within 4Å: Chain B: C.70, C.107, C.113, C.117 Ligands: ZN.7, ZN.9 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.70, B:C.107, B:C.113, B:C.117 ZN.9: 7 residues within 4Å: Chain B: C.64, C.66, C.70, C.75, C.107 Ligands: ZN.7, ZN.8 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.64, B:C.66, B:C.70, B:C.75 ZN.10: 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

2 x SFG: SINEFUNGIN(Non-covalent)

SFG.5: 16 residues within 4Å: Chain A: M.138, G.139, W.140, S.174, Y.175, R.199, F.200, N.202, H.203, Y.244, W.249, F.256, T.257, C.258, Q.259 Ligands: 01.6 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:W.140, A:S.174, A:Y.175, A:R.199, A:N.202, A:H.203, A:H.203, A:Q.259 SFG.11: 16 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.256, T.257, C.258, Q.259 Ligands: 01.12 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:Y.175, B:Y.244 Hydrogen bonds: B:M.138, B:W.140, B:S.174, B:Y.175, B:Y.175, B:R.199, B:H.203, B:H.203, B:Y.244, B:Q.259

2 x 01: ~{N}-[(2~{S})-1-[[6-(1-methylpiperidin-4-yl)oxypyridin-3-yl]amino]-1-oxidanylidene-hexan-2-yl]-3-(pyridin-4-ylamino)benzamide

01.6: 18 residues within 4Å: Chain A: I.99, E.100, D.164, A.167, D.168, D.173, S.174, L.176, F.177, D.178, P.211, R.213, F.242, D.243, Y.244, R.247, F.248 Ligands: SFG.5 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:A.167, A:L.176, A:F.242, A:F.242, A:Y.244, A:Y.244, A:Y.244, A:Y.244, A:R.247 Hydrogen bonds: A:D.168, A:L.176, A:D.178, A:D.178, A:R.213, A:R.213, A:Y.244, A:R.247 Water bridges: A:F.248 01.12: 17 residues within 4Å: Chain B: I.99, Y.157, D.164, A.167, D.168, D.173, S.174, Y.175, L.176, F.177, D.178, P.211, R.213, D.243, Y.244, R.247 Ligands: SFG.11 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:A.167, B:D.173, B:L.176, B:L.176, B:D.178, B:P.211, B:Y.244, B:Y.244 Hydrogen bonds: B:L.176, B:D.178, B:D.178, B:R.213, B:R.213, B:Y.244, B:R.247, B:R.247 pi-Cation interactions: B:R.247

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nishigaya, Y. et al., Discovery of potent substrate-type lysine methyltransferase G9a inhibitors for the treatment of sickle cell disease. Eur.J.Med.Chem. (2025)

Release Date

2025-05-21

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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