SMTL ID : 6bgy.1

LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR 2-((2-chlorophenyl)(2-(1-methylpyrrolidin-2-yl)ethoxy)methyl)-1H-pyrrolo[3,2-b]pyridine-7-carboxylic acid(Compound 46)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.22 Å

Oligo State

monomer

Ligands

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

DLJ.1: 17 residues within 4Å: Chain A: R.75, Y.151, A.153, D.154, Y.214, S.221, F.222, C.223, H.225, I.226, D.228, N.235, K.243, W.245, H.313 Ligands: MN.2, EDO.5 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.245 Hydrogen bonds: A:Y.151 Salt bridges: 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: DLJ.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.1, H2O.3

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

EDO.3: 2 residues within 4Å: Chain A: N.298, C.300 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.298 Water bridges: A:K.52, A:R.54, A:R.54, A:T.129, A:T.129, A:R.296 EDO.4: 3 residues within 4Å: Chain A: E.25, P.55, K.57 3 PLIP interactions: 3 interactions with chain A Water bridges: A:E.25, A:P.55, A:K.57 EDO.5: 6 residues within 4Å: Chain A: Q.77, S.221, F.222, C.223, I.281 Ligands: DLJ.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.77, A:S.221, A:C.223 Water bridges: A:R.75, A:F.222 EDO.6: 3 residues within 4Å: Chain A: S.250, P.309, R.310 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.250, A:S.250

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

DMS.7: 1 residues within 4Å: Chain A: M.126 No protein-ligand interaction detected (PLIP) DMS.8: 5 residues within 4Å: Chain A: C.65, E.66, V.67, K.68, R.171 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.67, A:R.171

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 5 residues within 4Å: Chain A: E.227, D.228, H.229, W.230, L.274 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.228, A:H.229 Water bridges: A:E.227, A:D.228, A:D.228

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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