SMTL ID : 6mbp.1

GLP Methyltransferase with Inhibitor EML741- P3121 Crystal Form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

2 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: 17 residues within 4Å: Chain A: Y.150, D.157, A.160, D.161, R.163, D.166, S.167, L.169, D.171, D.173, V.179, F.235, Y.237, R.240, F.241, I.244, K.245 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Y.150, A:D.157, A:A.160, A:L.169, A:V.179, A:V.179, A:F.235, A:I.244 Hydrogen bonds: A:D.166, A:D.166 Water bridges: A:L.169, A:F.241 pi-Cation interactions: A:Y.237 JDG.14: 19 residues within 4Å: Chain B: Y.150, D.157, A.160, D.161, R.163, E.164, D.166, S.167, L.169, D.171, D.173, V.179, F.235, Y.237, R.240, F.241, I.244, K.245 Ligands: EDO.21 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:Y.150, B:D.157, B:L.169, B:V.179, B:F.235, B:I.244 Hydrogen bonds: B:D.166, B:D.166 Water bridges: B:F.241 pi-Cation interactions: B:Y.237

8 x ZN: ZINC ION(Non-covalent)

ZN.2: 7 residues within 4Å: Chain A: C.57, C.63, C.100, C.106, C.110 Ligands: ZN.3, 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.3: 6 residues within 4Å: Chain A: C.57, C.70, C.100, C.104 Ligands: ZN.2, 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.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.15: 6 residues within 4Å: Chain B: C.57, C.59, C.63, C.68 Ligands: ZN.16, ZN.17 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.57, B:C.59, B:C.63, B:C.68 ZN.16: 6 residues within 4Å: Chain B: C.63, C.100, C.106, C.110 Ligands: ZN.15, ZN.17 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.63, B:C.100, B:C.106, B:C.110 ZN.17: 6 residues within 4Å: Chain B: C.57, C.70, C.100, C.104 Ligands: ZN.15, ZN.16 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.57, B:C.70, B:C.100, B:C.104 ZN.18: 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.6: 17 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 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:W.133, A:W.133, A:S.167, A:S.167, A:Y.168, A:Y.168, A:N.195, A:H.196, A:H.196, A:R.252 SAH.19: 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.249, S.250, C.251, R.252, C.253 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:W.133, B:W.133, B:S.167, B:S.167, B:Y.168, B:Y.168, B:N.195, B:H.196, B:H.196, B:R.252 Water bridges: B:R.127

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

EDO.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:D.61, A:S.65 EDO.8: 6 residues within 4Å: Chain A: N.39, I.47, L.154, H.211, F.216, R.218 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.39, A:F.216 Water bridges: A:N.39, A:R.218, A:R.218 EDO.9: 4 residues within 4Å: Chain A: M.91, A.92, P.200, T.224 No protein-ligand interaction detected (PLIP) EDO.10: 5 residues within 4Å: Chain A: G.12, Y.13, E.14, R.15 Chain B: R.108 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.108 Water bridges: B:R.108 EDO.11: 4 residues within 4Å: Chain A: K.34, Y.187 Chain B: Y.56, A.103 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.187, A:Y.187 Water bridges: A:K.34, A:K.34 EDO.12: 3 residues within 4Å: Chain A: Y.56, A.103 Chain B: K.34 4 PLIP interactions: 4 interactions with chain A Water bridges: A:I.51, A:T.52, A:A.103, A:C.104 EDO.13: 7 residues within 4Å: Chain A: R.11, Y.13, K.34, Y.35 Chain B: C.104, S.105, C.106 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:C.106, A:Y.35 Water bridges: A:K.34 EDO.20: 5 residues within 4Å: Chain B: D.82, R.113, V.114, N.117, R.120 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.82, B:N.117 EDO.21: 4 residues within 4Å: Chain B: F.170, D.236, Y.237 Ligands: JDG.14 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.236 EDO.22: 7 residues within 4Å: Chain A: Y.13 Chain B: N.101, H.102, R.108, R.113, Q.116, A.210 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:H.102, B:H.102, B:R.108, B:R.113 Water bridges: B:R.108, B:Q.116 EDO.23: 3 residues within 4Å: Chain B: D.80, K.81, R.111 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.81, B:R.111, B:R.111 Water bridges: B:D.80 EDO.24: 5 residues within 4Å: Chain B: C.59, I.60, D.61, S.65, N.67 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:I.60, B:D.61, B:S.65, B:S.65, B:N.67 Water bridges: B:V.58

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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