SMTL ID : 6bh1.1

LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR (S)-2-((2-chlorophenyl)(2-(piperidin-1-yl)ethoxy)methyl)-1l2-pyrrolo[3,2-b]pyridine-7-carboxylic acid (Compound N52)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

monomer

Ligands

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

DQG.1: 15 residues within 4Å: Chain A: R.75, 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 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.212, A:W.245 Hydrogen bonds: A:Y.151 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: DQG.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

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

DMS.3: 1 residues within 4Å: Chain A: A.99 No protein-ligand interaction detected (PLIP)

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

EDO.4: 3 residues within 4Å: Chain A: F.63, H.238, W.239 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.61 EDO.5: 3 residues within 4Å: Chain A: K.47, H.251, Y.295 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.47

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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