SMTL ID : 6mbo.1

GLP Methyltransferase with Inhibitor EML741-P212121 Crystal Form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.59 Å

Oligo State

homo-dimer

Ligands

4 x JDG: 2-cyclohexyl-7-methoxy-N-[1-(propan-2-yl)piperidin-4-yl]-8-[3-(pyrrolidin-1-yl)propoxy]-3H-1,4-benzodiazepin-5-amine(Non-covalent)

JDG.1: 7 residues within 4Å: Chain A: T.52, Y.56, A.103 Chain B: K.34, R.185, F.186, Y.187 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:Y.56, A:A.103, B:K.34, B:F.186, B:Y.187 Water bridges: B:Y.187 JDG.2: 19 residues within 4Å: Chain A: Y.150, D.157, A.160, D.161, R.163, D.166, S.167, L.169, F.170, D.171, V.179, Y.180, C.181, F.235, Y.237, R.240, F.241, I.244, K.245 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.150, A:A.160, A:L.169, A:F.170, A:V.179, A:F.235, A:I.244 Hydrogen bonds: A:D.166 Water bridges: A:L.169, A:F.241 Salt bridges: A:D.166 pi-Cation interactions: A:Y.237 JDG.16: 7 residues within 4Å: Chain B: I.60, D.61, D.62, K.81, W.107, N.109, R.111 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:W.107 Water bridges: B:S.64 JDG.17: 19 residues within 4Å: Chain B: Y.150, D.157, A.160, D.161, R.163, D.166, S.167, L.169, F.170, D.171, V.179, C.181, F.235, Y.237, R.240, F.241, I.244, K.245 Ligands: EDO.28 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:Y.150, B:D.157, B:A.160, B:L.169, B:F.170, B:V.179, B:F.235, B:I.244 Hydrogen bonds: B:D.166, B:D.166 Water bridges: B:L.169 Salt bridges: B:D.166 pi-Cation interactions: B:Y.237

8 x ZN: ZINC ION(Non-covalent)

ZN.3: 7 residues within 4Å: Chain A: C.57, C.63, C.100, C.106, C.110 Ligands: ZN.4, ZN.5 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.70, C.100, C.104 Ligands: ZN.3, ZN.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.57, A:C.70, A:C.100, A:C.104 ZN.5: 6 residues within 4Å: Chain A: C.57, C.59, C.63, C.68 Ligands: ZN.3, ZN.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.57, A:C.59, A:C.63, A:C.68 ZN.6: 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.18: 6 residues within 4Å: Chain B: C.57, C.59, C.63, C.68 Ligands: ZN.19, ZN.20 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.57, B:C.59, B:C.63, B:C.68 ZN.19: 7 residues within 4Å: Chain B: C.57, C.63, C.100, C.106, C.110 Ligands: ZN.18, ZN.20 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.63, B:C.100, B:C.106, B:C.110 ZN.20: 6 residues within 4Å: Chain B: C.57, C.70, C.100, C.104 Ligands: ZN.18, ZN.19 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.57, B:C.70, B:C.100, B:C.104 ZN.21: 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 SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.7: 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, F.249, S.250, C.251, R.252, C.253 Ligands: EDO.9 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:W.133, A:W.133, A:S.167, A:Y.168, A:Y.168, A:N.195, A:H.196, A:H.196, A:R.252 Water bridges: A:S.167 SAH.22: 16 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 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:W.133, B:W.133, B:S.167, B:Y.168, B:N.195, B:H.196, B:H.196, B:Y.237, B:R.252, B:C.253 Water bridges: B:R.127, B:S.167

14 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.8: 6 residues within 4Å: Chain A: R.127, T.128, R.129, D.130, M.131, G.132 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.128, A:G.132 EDO.9: 3 residues within 4Å: Chain A: F.249, R.252 Ligands: SAH.7 No protein-ligand interaction detected (PLIP) EDO.10: 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 EDO.11: 6 residues within 4Å: Chain A: N.39, I.47, L.154, H.211, F.216, R.218 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.39, A:F.216, A:R.218 Water bridges: A:N.39, A:R.218, A:R.218 EDO.12: 2 residues within 4Å: Chain A: R.7, P.17 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.7, A:R.7 EDO.13: 3 residues within 4Å: Chain A: G.12 Chain B: W.107, N.109 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.8 EDO.14: 6 residues within 4Å: Chain A: R.49 Chain B: N.39, V.41, I.47, R.49 Ligands: EDO.23 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.49 Water bridges: B:V.41 EDO.15: 5 residues within 4Å: Chain A: P.30, S.31, Y.33, K.34, Y.35 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.31, A:Y.35 Water bridges: A:R.11 EDO.23: 7 residues within 4Å: Chain B: N.39, I.47, L.154, H.211, F.216, R.218 Ligands: EDO.14 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.39, B:F.216 Water bridges: B:N.39, B:R.218, B:R.218, B:R.218 EDO.24: 5 residues within 4Å: Chain B: G.246, K.247, L.248, F.249, S.250 No protein-ligand interaction detected (PLIP) EDO.25: 5 residues within 4Å: Chain B: P.30, S.31, Y.33, K.34, Y.35 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.31, B:Y.35 Water bridges: B:K.34 EDO.26: 5 residues within 4Å: Chain B: R.120, A.121, Q.139, P.142, T.145 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.139, B:T.145 Water bridges: B:R.84 EDO.27: 7 residues within 4Å: Chain B: D.25, R.127, T.128, R.129, D.130, M.131, G.132 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.25, B:G.132 Water bridges: B:D.130, B:M.131 EDO.28: 5 residues within 4Å: Chain B: F.170, F.235, D.236, Y.237 Ligands: JDG.17 1 PLIP interactions: 1 interactions with chain B Water bridges: B:D.171

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Milite, C. et al., Discovery of a Novel Chemotype of Histone Lysine Methyltransferase EHMT1/2 (GLP/G9a) Inhibitors: Rational Design, Synthesis, Biological Evaluation, and Co-crystal Structure. J. Med. Chem. (2019)

Release Date

2019-02-27

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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