SMTL ID : 3k5k.3 (2 other biounits)

Discovery of a 2,4-Diamino-7-aminoalkoxy-quinazoline as a Potent Inhibitor of Histone Lysine Methyltransferase, G9a

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 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.10: 6 residues within 4Å: Chain B: C.64, C.77, C.107, C.111 Ligands: ZN.11, ZN.12 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.64, B:C.77, B:C.107, B:C.111 ZN.11: 6 residues within 4Å: Chain B: C.70, C.107, C.113, C.117 Ligands: ZN.10, ZN.12 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.70, B:C.107, B:C.113, B:C.117 ZN.12: 6 residues within 4Å: Chain B: C.64, C.66, C.70, C.75 Ligands: ZN.10, ZN.11 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.64, B:C.66, B:C.70, B:C.75 ZN.13: 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: 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 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:W.140, A:W.140, A:W.140, A:S.174, A:N.202, A:H.203, A:H.203, A:Q.259 SAH.14: 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 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:W.140, B:W.140, B:W.140, B:S.174, B:N.202, B:H.203, B:H.203, B:Q.259 pi-Stacking: B:W.249

2 x DXQ: 7-[3-(dimethylamino)propoxy]-6-methoxy-2-(4-methyl-1,4-diazepan-1-yl)-N-(1-methylpiperidin-4-yl)quinazolin-4-amine(Non-covalent)

DXQ.6: 16 residues within 4Å: Chain A: D.164, A.167, D.168, R.170, D.173, S.174, L.176, D.178, C.188, F.242, Y.244, R.247, F.248, I.251, K.252 Ligands: UNX.9 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.176, A:L.176, A:R.247, A:I.251 Hydrogen bonds: A:D.173, A:D.173 Water bridges: A:L.176 Salt bridges: A:D.164, A:D.168, A:D.168 pi-Cation interactions: A:Y.244 DXQ.15: 16 residues within 4Å: Chain B: D.164, A.167, D.168, R.170, D.173, S.174, L.176, F.177, D.178, C.188, F.242, Y.244, F.248, I.251, K.252 Ligands: UNX.18 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:L.176, B:I.251 Hydrogen bonds: B:D.173 Water bridges: B:Y.157, B:L.176, B:F.248 Salt bridges: B:D.164, B:D.168, B:D.168 pi-Cation interactions: B:Y.244

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

CL.7: 2 residues within 4Å: Chain A: N.53, R.222 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain A: C.13, R.14 Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain A: T.51, N.53 Chain B: N.53 Ligand excluded by PLIP CL.17: 2 residues within 4Å: Chain B: C.13, R.14 Ligand excluded by PLIP

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

UNX.9: 1 residues within 4Å: Ligands: DXQ.6 No protein-ligand interaction detected (PLIP) UNX.18: 1 residues within 4Å: Ligands: DXQ.15 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, F. et al., Discovery of a 2,4-diamino-7-aminoalkoxyquinazoline as a potent and selective inhibitor of histone lysine methyltransferase G9a. J.Med.Chem. (2009)

Release Date

2009-11-10

Peptides

Histone-lysine N-methyltransferase, H3 lysine-9 specific 3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Histone-lysine N-methyltransferase, H3 lysine-9 specific 3

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