SMTL ID : 3rjw.1

Crystal structure of histone lysine methyltransferase g9a with an inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.56 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.23: 6 residues within 4Å: Chain B: C.64, C.77, C.107, C.111 Ligands: ZN.24, ZN.25 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.64, B:C.77, B:C.107, B:C.111 ZN.24: 6 residues within 4Å: Chain B: C.70, C.107, C.113, C.117 Ligands: ZN.23, ZN.25 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.70, B:C.107, B:C.113, B:C.117 ZN.25: 6 residues within 4Å: Chain B: C.64, C.66, C.70, C.75 Ligands: ZN.23, ZN.24 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.64, B:C.66, B:C.70, B:C.75 ZN.26: 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 SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.5: 18 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, C.260 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:W.140, A:W.140, A:W.140, A:N.202, A:H.203, A:H.203, A:Q.259, A:C.260 Water bridges: A:Y.175 SAH.27: 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 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:W.140, B:W.140, B:W.140, B:S.174, B:Y.175, B:N.202, B:H.203, B:H.203, B:Q.259, B:C.260 pi-Stacking: B:W.249

2 x CIQ: 2-cyclohexyl-6-methoxy-N-[1-(1-methylethyl)piperidin-4-yl]-7-(3-pyrrolidin-1-ylpropoxy)quinazolin-4-amine(Non-covalent)

CIQ.6: 14 residues within 4Å: Chain A: Y.157, D.164, A.167, D.168, R.170, D.173, S.174, L.176, F.177, D.178, F.242, Y.244, F.248, I.251 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.157, A:D.164, A:A.167, A:L.176, A:L.176 Hydrogen bonds: A:D.173, A:D.173 pi-Cation interactions: A:Y.244 CIQ.28: 16 residues within 4Å: Chain B: Y.157, D.164, A.167, D.168, R.170, D.173, S.174, Y.175, L.176, F.177, D.178, F.242, Y.244, F.248, I.251 Ligands: UNX.40 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:Y.157, B:D.164, B:A.167, B:L.176, B:L.176 Hydrogen bonds: B:D.173 Salt bridges: B:D.168

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

UNX.7: 2 residues within 4Å: Chain A: C.13, R.14 Ligand excluded by PLIP UNX.8: 5 residues within 4Å: Chain A: I.126, K.127, V.128, F.153, I.154 Ligand excluded by PLIP UNX.9: 4 residues within 4Å: Chain A: N.46, E.48, R.56 Ligands: UNX.22 Ligand excluded by PLIP UNX.10: 1 residues within 4Å: Chain A: E.21 Ligand excluded by PLIP UNX.11: 6 residues within 4Å: Chain A: N.97, K.98, E.100, P.101, P.102 Ligands: UNX.19 Ligand excluded by PLIP UNX.12: 6 residues within 4Å: Chain A: C.77, S.81, C.84, I.104, F.105, N.119 Ligand excluded by PLIP UNX.13: 6 residues within 4Å: Chain A: V.23, P.24, I.25, P.26, R.129, L.130 Ligand excluded by PLIP UNX.14: 3 residues within 4Å: Chain A: G.19, Y.20, E.21 Ligand excluded by PLIP UNX.15: 3 residues within 4Å: Chain A: Q.123, R.225 Ligands: UNX.16 Ligand excluded by PLIP UNX.16: 3 residues within 4Å: Chain A: Q.123, R.225 Ligands: UNX.15 Ligand excluded by PLIP UNX.17: 2 residues within 4Å: Chain A: N.53, R.222 Ligand excluded by PLIP UNX.18: 4 residues within 4Å: Chain A: F.96, N.97, K.98, I.99 Ligand excluded by PLIP UNX.19: 5 residues within 4Å: Chain A: W.85, F.96, N.97, P.102 Ligands: UNX.11 Ligand excluded by PLIP UNX.20: 6 residues within 4Å: Chain A: V.214, F.215, M.216, H.218, F.223, R.225 Ligand excluded by PLIP UNX.21: 1 residues within 4Å: Chain A: E.45 Ligand excluded by PLIP UNX.22: 4 residues within 4Å: Chain A: C.47, E.48 Chain B: R.56 Ligands: UNX.9 Ligand excluded by PLIP UNX.29: 5 residues within 4Å: Chain B: P.101, P.102, L.103, V.212, R.213 Ligand excluded by PLIP UNX.30: 5 residues within 4Å: Chain B: F.215, M.216, L.217, H.218 Ligands: UNX.36 Ligand excluded by PLIP UNX.31: 2 residues within 4Å: Chain A: E.45 Chain B: E.45 Ligand excluded by PLIP UNX.32: 1 residues within 4Å: Chain B: Y.193 Ligand excluded by PLIP UNX.33: 2 residues within 4Å: Chain B: N.22, G.125 Ligand excluded by PLIP UNX.34: 2 residues within 4Å: Chain B: Q.123, R.225 Ligand excluded by PLIP UNX.35: 3 residues within 4Å: Chain B: D.68, D.69, C.117 Ligand excluded by PLIP UNX.36: 7 residues within 4Å: Chain B: V.214, F.215, H.218, F.223, P.224, R.225 Ligands: UNX.30 Ligand excluded by PLIP UNX.37: 5 residues within 4Å: Chain B: C.66, D.68, C.70, S.71, S.72 Ligand excluded by PLIP UNX.38: 7 residues within 4Å: Chain B: D.15, A.17, G.19, Y.20, E.21, V.23, P.24 Ligand excluded by PLIP UNX.39: 3 residues within 4Å: Chain B: T.135, A.136, G.139 Ligand excluded by PLIP UNX.40: 3 residues within 4Å: Chain B: D.178, R.247 Ligands: CIQ.28 Ligand excluded by PLIP UNX.41: 4 residues within 4Å: Chain B: N.46, L.161, H.218, R.225 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vedadi, M. et al., A chemical probe selectively inhibits G9a and GLP methyltransferase activity in cells. Nat.Chem.Biol. (2011)

Release Date

2011-05-04

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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