SMTL ID : 5ttf.1 (1 other biounit)

Crystal structure of catalytic domain of G9a with MS012

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.72 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: 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

2 x SAM: S-ADENOSYLMETHIONINE(Non-covalent)

SAM.5: 16 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, F.256, T.257, C.258, Q.259 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:W.140, A:S.174, A:Y.175, A:Y.175, A:N.202, A:N.202, A:H.203, A:H.203, A:Q.259 Water bridges: A:R.134, A:S.174 SAM.13: 18 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, C.260 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:W.140, B:S.174, B:Y.175, B:Y.175, B:N.202, B:N.202, B:H.203, B:H.203, B:Q.259 pi-Stacking: B:W.249

2 x 7KZ: N4-(1-methylpiperidin-4-yl)-N2-hexyl-6,7-dimethoxyquinazoline-2,4-diamine(Non-covalent)

7KZ.6: 11 residues within 4Å: Chain A: A.167, D.168, R.170, D.173, L.176, D.178, C.188, R.247, F.248, I.251, K.252 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.176, A:I.251 Hydrogen bonds: A:D.173, A:D.173 Water bridges: A:F.248 pi-Cation interactions: A:R.247 7KZ.14: 11 residues within 4Å: Chain B: A.167, D.168, R.170, D.173, L.176, D.178, C.188, R.247, F.248, I.251, K.252 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.176, B:I.251 Hydrogen bonds: B:D.168, B:D.173, B:D.173 Water bridges: B:F.248

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

CL.7: 2 residues within 4Å: Chain A: N.53, R.222 Ligand excluded by PLIP

2 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.8: 3 residues within 4Å: Chain A: Q.62, H.63, L.76 No protein-ligand interaction detected (PLIP) UNX.15: 5 residues within 4Å: Chain B: V.31, Y.133, R.134, T.135, A.136 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xiong, Y. et al., Discovery of Potent and Selective Inhibitors for G9a-Like Protein (GLP) Lysine Methyltransferase. J. Med. Chem. (2017)

Release Date

2016-12-21

Peptides

Histone-lysine N-methyltransferase EHMT2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Histone-lysine N-methyltransferase EHMT2

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