SMTL ID : 5iw0.1

Linked KDM5A Jmj Domain Bound to the Inhibitor N19 [2-(5-((4-chloro-2-methylbenzyl)oxy)-1H-pyrazol-1-yl)isonicotinic acid]

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.63 Å

Oligo State

monomer

Ligands

1 x 6EP: 2-{5-[(4-chloro-2-methylphenyl)methoxy]-1H-pyrazol-1-yl}pyridine-4-carboxylic acid(Non-covalent)

6EP.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, E.227, N.235, K.243, W.245, H.313 Ligands: AKG.2, MN.3 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.151, A:F.222, A:W.245 Hydrogen bonds: A:Y.151 Water bridges: A:Y.214 Salt bridges: A:K.243 pi-Stacking: A:F.222, A:H.225

1 x AKG: 2-OXOGLUTARIC ACID(Non-covalent)

AKG.2: 6 residues within 4Å: Chain A: F.222, C.223, H.225, Q.277, L.278 Ligands: 6EP.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:C.223 Salt bridges: A:H.225

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

MN.3: 4 residues within 4Å: Chain A: H.225, E.227, H.313 Ligands: 6EP.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.3

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

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: 5 residues within 4Å: Chain A: V.140, S.141, I.281, M.282, N.283 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.283

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 3 residues within 4Å: Chain A: D.228, H.229, W.230 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.229 GOL.7: 5 residues within 4Å: Chain A: Q.77, R.78, L.79, E.81, S.221 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.81, A:S.221, A:S.221 Water bridges: A:R.78, A:E.81

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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