SMTL ID : 5ivc.1

Linked KDM5A Jmj Domain Bound to the Inhibitor N3 (4'-[(2-phenylethyl)carbamoyl][2,2'-bipyridine]-4-carboxylic acid)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.57 Å

Oligo State

monomer

Ligands

1 x 6E7: 4'-[(2-phenylethyl)carbamoyl][2,2'-bipyridine]-4-carboxylic acid(Non-covalent)

6E7.1: 14 residues within 4Å: Chain A: R.75, Q.77, Y.151, A.153, Y.214, S.221, F.222, H.225, E.227, N.235, K.243, W.245, H.313 Ligands: MN.2 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.151, A:A.153, A:Y.214, A:F.222, A:W.245 Hydrogen bonds: A:Y.151 Water bridges: A:N.327 Salt bridges: A:K.243 pi-Stacking: A:F.222

1 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 4 residues within 4Å: Chain A: H.225, E.227, H.313 Ligands: 6E7.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.225, A:E.227, A:H.313, H2O.5

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

EDO.3: 2 residues within 4Å: Chain A: R.75, L.278 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.75, A:R.75 EDO.4: 4 residues within 4Å: Chain A: E.66, V.67, K.68, R.171 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.67, A:K.68 EDO.5: 4 residues within 4Å: Chain A: S.141, I.281, M.282, N.283 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.283 Water bridges: A:E.83

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 4 residues within 4Å: Chain A: E.227, D.228, H.229, W.230 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.228, A:H.229, A:H.229

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Horton, J.R. et al., Structural Basis for KDM5A Histone Lysine Demethylase Inhibition by Diverse Compounds. Cell Chem Biol (2016)

Release Date

2016-07-27

Peptides

Lysine-specific demethylase 5A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lysine-specific demethylase 5A

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