SMTL ID : 6bh5.1

LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR 2-((2-chlorophenyl)(3-(piperidin-1-yl)propoxy)methyl)-1H-pyrrolo[3,2-b]pyridine-7-carboxylic acid (Compound N48)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

monomer

Ligands

1 x DNY: 2-{(S)-(2-chlorophenyl)[3-(piperidin-1-yl)propoxy]methyl}-1H-pyrrolo[3,2-b]pyridine-7-carboxylic acid(Non-covalent)

DNY.1: 16 residues within 4Å: Chain A: R.75, Y.151, A.153, Y.214, S.221, F.222, C.223, H.225, I.226, D.228, N.235, K.243, W.245, L.274, H.313 Ligands: MN.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.245, A:L.274 Hydrogen bonds: A:Y.151 Water bridges: A:R.75 Salt bridges: A:E.227, A:D.228, 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: DNY.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.3

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

EDO.3: 2 residues within 4Å: Chain A: D.228, H.229 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.228, A:H.229 EDO.4: 3 residues within 4Å: Chain A: K.52, R.54, N.298 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:K.52, A:R.54 Water bridges: A:K.52, A:T.129, A:R.296, A:N.298, A:N.298, A:N.298, A:N.298 EDO.5: 3 residues within 4Å: Chain A: E.145, D.146, V.147 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.145, A:E.145 EDO.6: 1 residues within 4Å: Chain A: M.126 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.126 EDO.7: 3 residues within 4Å: Chain A: H.229, W.230, P.309 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.230

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 5 residues within 4Å: Chain A: Q.77, R.78, L.79, E.81, S.221 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.81, A:S.221 Water bridges: A:Q.77, A:R.78, A:R.78, A:E.81, A:L.278

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Horton, J.R. et al., Insights into the Action of Inhibitor Enantiomers against Histone Lysine Demethylase 5A. J. Med. Chem. (2018)

Release Date

2018-03-28

Peptides

Lysine-specific demethylase 5A, linked KDM5A JMJ domain: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lysine-specific demethylase 5A, linked KDM5A JMJ domain

Related Entries With Identical Sequence