SMTL ID : 6bh0.1

LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR (R)-2-((2-chlorophenyl)(2-(piperidin-1-yl)ethoxy)methyl)-1l2-pyrrolo[3,2-b]pyridine-7-carboxylic acid (Compound N51)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

monomer

Ligands

1 x DO1: 2-{(R)-(2-chlorophenyl)[2-(piperidin-1-yl)ethoxy]methyl}-1H-pyrrolo[3,2-b]pyridine-7-carboxylic acid(Non-covalent)

DO1.1: 16 residues within 4Å: Chain A: R.75, Q.77, Y.151, A.153, D.154, W.212, Y.214, S.221, F.222, C.223, H.225, N.235, K.243, W.245, H.313 Ligands: MN.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:A.153, A:W.212, A:F.222, A:W.245 Hydrogen bonds: A:Y.151 Water bridges: A:Y.214, A:K.243 Salt bridges: A:D.154, 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: DO1.1 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 DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.3: 2 residues within 4Å: Chain A: S.250, P.309 No protein-ligand interaction detected (PLIP)

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

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