SMTL ID : 5vsf.1

Structure of human GLP SET-domain (EHMT1) in complex with inhibitor 17

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

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

SAM.1: 18 residues within 4Å: Chain A: M.131, G.132, W.133, S.167, Y.168, R.192, F.193, I.194, N.195, H.196, Y.237, F.241, W.242, F.249, S.250, C.251, R.252, C.253 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:W.133, A:S.167, A:Y.168, A:N.195, A:N.195, A:H.196, A:H.196, A:H.196, A:R.252 Water bridges: A:S.167 SAM.9: 17 residues within 4Å: Chain B: M.131, G.132, W.133, S.167, Y.168, R.192, F.193, I.194, N.195, H.196, Y.237, F.241, F.249, S.250, C.251, R.252, C.253 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:W.133, B:S.167, B:Y.168, B:N.195, B:N.195, B:H.196, B:H.196, B:Y.237, B:R.252 Water bridges: B:S.167

8 x ZN: ZINC ION(Non-covalent)

ZN.2: 6 residues within 4Å: Chain A: C.57, C.70, C.100, C.104 Ligands: ZN.3, ZN.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.57, A:C.70, A:C.100, A:C.104 ZN.3: 7 residues within 4Å: Chain A: C.57, C.63, C.100, C.106, C.110 Ligands: ZN.2, ZN.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.63, A:C.100, A:C.106, A:C.110 ZN.4: 6 residues within 4Å: Chain A: C.57, C.59, C.63, C.68 Ligands: ZN.2, ZN.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.57, A:C.59, A:C.63, A:C.68 ZN.5: 4 residues within 4Å: Chain A: C.198, C.251, C.253, C.258 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.198, A:C.251, A:C.253, A:C.258 ZN.10: 6 residues within 4Å: Chain B: C.57, C.70, C.100, C.104 Ligands: ZN.11, ZN.12 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.57, B:C.70, B:C.100, B:C.104 ZN.11: 7 residues within 4Å: Chain B: C.57, C.63, C.100, C.106, C.110 Ligands: ZN.10, ZN.12 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.63, B:C.100, B:C.106, B:C.110 ZN.12: 6 residues within 4Å: Chain B: C.57, C.59, C.63, C.68 Ligands: ZN.10, ZN.11 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.57, B:C.59, B:C.63, B:C.68 ZN.13: 4 residues within 4Å: Chain B: C.198, C.251, C.253, C.258 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.198, B:C.251, B:C.253, B:C.258

2 x 9HG: N~2~-cyclopentyl-6,7-dimethoxy-N~2~-methyl-N~4~-(1-methylpiperidin-4-yl)quinazoline-2,4-diamine(Non-covalent)

9HG.6: 14 residues within 4Å: Chain A: D.157, A.160, D.161, R.163, D.166, L.169, D.171, V.179, C.181, Y.237, R.240, F.241, I.244, K.245 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:D.157, A:L.169, A:V.179, A:I.244 Hydrogen bonds: A:D.166 Water bridges: A:F.241 Salt bridges: A:D.166 9HG.14: 12 residues within 4Å: Chain B: D.157, A.160, D.161, R.163, D.166, L.169, D.171, V.179, R.240, F.241, I.244, K.245 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:D.157, B:L.169, B:V.179, B:I.244 Hydrogen bonds: B:D.166 Water bridges: B:F.241 Salt bridges: B:D.166

1 x DIO: 1,4-DIETHYLENE DIOXIDE(Non-covalent)

DIO.7: 5 residues within 4Å: Chain A: C.59, I.60, D.61, S.65, N.67 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.60, A:S.65

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 5 residues within 4Å: Chain A: N.39, V.41, I.47, R.49 Chain B: R.49 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.39, A:R.49, B:R.49 GOL.15: 4 residues within 4Å: Chain A: R.49 Chain B: V.41, I.47, R.49 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.39, B:R.49 Water bridges: B:N.46, B:I.47, B:R.49

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xiong, Y. et al., Structure-activity relationship studies of G9a-like protein (GLP) inhibitors. Bioorg. Med. Chem. (2017)

Release Date

2017-07-12

Peptides

Histone-lysine N-methyltransferase EHMT1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Histone-lysine N-methyltransferase EHMT1

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