SMTL ID : 6bgz.1

LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR 2-((2-chlorophenyl)(2-(1-methyl-1H-imidazol-2-yl)ethoxy)methyl)-1H-pyrrolo[3,2-b]pyridine-7-carboxylic acid (Compound N47)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.69 Å

Oligo State

monomer

Ligands

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

DNV.1: 15 residues within 4Å: Chain A: R.75, Y.151, A.153, Y.214, S.221, F.222, C.223, H.225, N.235, K.243, W.245, Q.277, L.278, H.313 Ligands: MN.2 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.245 Hydrogen bonds: A:Y.151 Water bridges: A:Y.214 Salt bridges: 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: DNV.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.5

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: E.227, D.228, H.229, W.230, L.274 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.229 Water bridges: A:I.226, A:E.227, A:Q.277 GOL.4: 6 residues within 4Å: Chain A: Q.77, R.78, L.79, E.81, S.221, I.281 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.79, A:S.221 Water bridges: A:V.76, A:R.78, A:E.81

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