SMTL ID : 5ylt.1

Crystal structure of SET7/9 in complex with a cyproheptadine derivative

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.69 Å

Oligo State

monomer

Ligands

1 x SFG: SINEFUNGIN(Non-covalent)

SFG.1: 14 residues within 4Å: Chain A: I.120, A.123, G.124, E.125, G.161, N.162, H.190, K.191, A.192, N.193, H.194, Y.232, W.249, E.253 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:Y.232 Hydrogen bonds: A:E.125, A:H.190, A:N.193, A:N.193, A:H.194, A:E.253 Water bridges: A:N.162, A:N.162, A:N.162, A:N.179, A:W.249 Salt bridges: A:K.191 pi-Stacking: A:W.249, A:W.249, A:W.249

1 x C7N: 2-(1-methylpiperidin-4-ylidene)tricyclo[9.4.0.0^{3,8}]pentadeca-1(11),3(8),4,6,9,12,14-heptaen-6-ol(Non-covalent)

C7N.2: 15 residues within 4Å: Chain A: Y.142, W.157, N.160, G.161, T.163, Y.202, Y.232, G.233, Y.234, D.235, P.238, P.239, P.247, W.249, Y.250 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.232, A:Y.232, A:P.238, A:P.247, A:W.249, A:W.249, A:Y.250 Hydrogen bonds: A:Y.234, A:D.235 Water bridges: A:Y.202 pi-Cation interactions: A:Y.232

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: A.158, L.159, N.160, G.161, N.162, V.174, P.175 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.161, A:N.162, A:V.174, A:E.176 Water bridges: A:N.162, A:N.162 GOL.4: 5 residues within 4Å: Chain A: V.113, Y.114, V.115, L.188 Ligands: GOL.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.113, A:V.115, A:V.115 GOL.5: 4 residues within 4Å: Chain A: Y.114, V.115, A.116 Ligands: GOL.4 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.117

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hirano, T. et al., Development of Novel Inhibitors for Histone Methyltransferase SET7/9 based on Cyproheptadine. ChemMedChem (2018)

Release Date

2018-06-20

Peptides

Histone-lysine N-methyltransferase SETD7: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Histone-lysine N-methyltransferase SETD7

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