SMTL ID : 6bh4.1

LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR 5-(1-(tert-butyl)-1H-pyrazol-4-yl)-6-isopropyl-7-oxo-4,7-dihydropyrazolo[1,5-a]pyrimidine-3-carbonitrile (Compound N75/CPI-48)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

monomer

Ligands

1 x DQS: 5-(1-tert-butyl-1H-pyrazol-4-yl)-7-oxo-6-(propan-2-yl)-4,7-dihydropyrazolo[1,5-a]pyrimidine-3-carbonitrile(Non-covalent)

DQS.1: 16 residues within 4Å: Chain A: R.75, Y.151, G.152, A.153, D.154, Y.214, S.220, S.221, F.222, H.225, N.235, K.243, W.245, H.313, N.317 Ligands: MN.2 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Y.151, A:Y.151, A:A.153, A:Y.214, A:F.222 Hydrogen bonds: A:Y.151, A:N.235, A:N.317 Water bridges: A:K.243 pi-Stacking: A:Y.214, A:Y.214, A:F.222, 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: DQS.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.1

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

EDO.3: 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 EDO.4: 6 residues within 4Å: Chain A: K.116, H.125, V.127, T.129, E.241, P.242 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.116, A:V.127 Water bridges: A:T.129 EDO.5: 2 residues within 4Å: Chain A: S.27, W.28 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.28 Water bridges: A:S.27, A:E.29 EDO.6: 1 residues within 4Å: Chain A: P.55 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.25, A:P.55 EDO.7: 5 residues within 4Å: Chain A: V.140, S.141, I.281, M.282, N.283 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.83, A:N.283 EDO.8: 6 residues within 4Å: Chain A: W.212, Y.214, E.227, A.325, V.326, N.327 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:W.212, A:E.227, A:N.327, A:N.327 Water bridges: A:S.233 EDO.9: 2 residues within 4Å: Chain A: M.126, P.128 No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 4 residues within 4Å: Chain A: E.227, D.228, H.229, W.230 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.229, A:W.230 Water bridges: 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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