SMTL ID : 6bgv.1

LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR 2-((2-chlorophenyl)(2-(piperidin-1-yl)ethoxy)methyl)-1l2-pyrrolo[3,2-b]pyridine-7-carboxylic acid (Compound N40)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.59 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: 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, EDO.12 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.212, A:F.222, A:F.222, 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.3, H2O.7

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: E.227, D.228, H.229, W.230 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.227, A:H.229 Water bridges: A:D.228, A:Q.277 GOL.4: 8 residues within 4Å: Chain A: L.82, E.83, V.140, S.141, I.281, M.282, N.283, V.286 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.83, A:V.140, A:N.283 Water bridges: A:I.281 GOL.5: 7 residues within 4Å: Chain A: E.257, M.260, D.273, H.276, Q.277, T.280, Y.312 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.276, A:Q.277 Water bridges: A:W.224, A:T.280 GOL.6: 2 residues within 4Å: Chain A: R.78, E.81 No protein-ligand interaction detected (PLIP)

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

DMS.7: 2 residues within 4Å: Chain A: F.63, W.239 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:W.239 DMS.8: 5 residues within 4Å: Chain A: C.65, E.66, V.67, K.68, R.171 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.68

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

EDO.9: 3 residues within 4Å: Chain A: K.47, H.251, Y.295 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.47, A:Y.295 EDO.10: 3 residues within 4Å: Chain A: E.25, P.55, K.57 No protein-ligand interaction detected (PLIP) EDO.11: 2 residues within 4Å: Chain A: E.254, Q.255 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.255 EDO.12: 6 residues within 4Å: Chain A: Q.77, S.221, F.222, C.223, I.281 Ligands: DQG.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.221 Water bridges: A:Q.77, A:E.81, A:F.222

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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