SMTL ID : 5ivj.1

Linked KDM5A Jmj Domain Bound to the Inhibitor N11 [3-({1-[2-(4,4-difluoropiperidin-1-yl)ethyl]-5-fluoro-1H-indazol-3-yl}amino)pyridine-4-carboxylic acid]

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.57 Å

Oligo State

monomer

Ligands

1 x 6ED: 3-({1-[2-(4,4-difluoropiperidin-1-yl)ethyl]-5-fluoro-1H-indazol-3-yl}amino)pyridine-4-carboxylic acid(Non-covalent)

6ED.1: 16 residues within 4Å: Chain A: R.75, Q.77, Y.151, A.153, D.154, Y.214, S.221, F.222, H.225, N.235, K.243, W.245, Q.277, L.278, H.313 Ligands: MN.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.151, A:A.153, A:Y.214, A:H.225, A:W.245 Hydrogen bonds: A:Y.151 Water bridges: A:Y.214 Salt bridges: A:E.227, A:K.243 pi-Stacking: A:F.222 Halogen bonds: A:Q.77

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

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

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: I.226, E.227, D.228, H.229, W.230 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.227, A:H.229

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.4: 4 residues within 4Å: Chain A: Q.106, G.109, E.110, D.113 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:D.113

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

Related Entries With Identical Sequence