SMTL ID : 5vsd.1

Structure of human GLP SET-domain (EHMT1) in complex with inhibitor 13

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 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 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:W.133, A:S.167, A:Y.168, A:Y.168, A:N.195, A:H.196, A:H.196, A:Y.237, A:R.252, A:C.253 Water bridges: A:R.127, A:S.167, A:R.252 SAM.8: 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 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:W.133, B:S.167, B:Y.168, B:Y.168, B:N.195, B:N.195, B:H.196, B:H.196, B:R.252, B:R.252, B:C.253 Water bridges: B:R.127, 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.9: 6 residues within 4Å: Chain B: C.57, C.70, C.100, C.104 Ligands: ZN.10, ZN.11 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.57, B:C.70, B:C.100, B:C.104 ZN.10: 7 residues within 4Å: Chain B: C.57, C.63, C.100, C.106, C.110 Ligands: ZN.9, ZN.11 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.63, B:C.100, B:C.106, B:C.110 ZN.11: 7 residues within 4Å: Chain B: C.57, C.59, C.63, C.68, C.100 Ligands: ZN.9, ZN.10 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.57, B:C.59, B:C.63, B:C.68 ZN.12: 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 9HJ: 6,7-dimethoxy-N~2~-methyl-N~4~-(1-methylpiperidin-4-yl)-N~2~-propylquinazoline-2,4-diamine(Non-covalent)

9HJ.6: 12 residues within 4Å: Chain A: D.157, A.160, D.161, R.163, D.166, L.169, D.171, C.181, R.240, F.241, I.244, K.245 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:D.157, A:D.166, A:L.169, A:L.169, A:I.244 Hydrogen bonds: A:D.166, A:D.166, A:R.240 Water bridges: A:F.241 9HJ.13: 12 residues within 4Å: Chain B: D.157, A.160, D.161, R.163, D.166, L.169, D.171, C.181, R.240, F.241, I.244, K.245 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:D.157, B:D.166, B:L.169, B:I.244 Hydrogen bonds: B:D.166, B:D.166, B:R.240 Water bridges: B:F.241

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.14: 5 residues within 4Å: Chain A: R.49 Chain B: N.39, C.40, R.49 Ligands: GOL.15 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.49 Water bridges: B:N.39, B:N.39, B:M.45 GOL.15: 8 residues within 4Å: Chain B: N.39, L.154, L.172, H.211, F.216, P.217, R.218 Ligands: GOL.14 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.39, B:H.211 Water bridges: B:N.39, B:E.149, B:R.218, B:R.218

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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