SMTL ID : 5f3c.1 (3 other biounits)

Crystal structure of human KDM4A in complex with compound 52d

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.06 Å

Oligo State

monomer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.189, E.191, H.277 Ligands: 5U8.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.189, A:E.191, A:H.277, H2O.1 ZN.2: 4 residues within 4Å: Chain A: C.235, H.241, C.307, C.309 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.235, A:H.241, A:C.307, A:C.309

1 x 5U8: 8-[4-[2-[(4-fluorophenyl)methyl-methyl-amino]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one(Non-covalent)

5U8.3: 15 residues within 4Å: Chain A: Y.133, D.136, E.170, G.171, Y.178, F.186, H.189, E.191, N.199, K.207, W.209, K.242, H.277, V.314 Ligands: ZN.1 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.186, A:W.209, A:K.242, A:V.314 Hydrogen bonds: A:Y.133, A:N.199 Water bridges: A:S.289, A:S.289 Salt bridges: A:D.136, A:D.192 pi-Stacking: A:F.186, A:H.189

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

DMS.4: 5 residues within 4Å: Chain A: Y.60, I.63, R.99, F.203, F.284 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.99 Salt bridges: A:D.64 DMS.5: 3 residues within 4Å: Chain A: Q.89, K.90, K.91 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.89 DMS.6: 2 residues within 4Å: Chain A: W.333, K.334 No protein-ligand interaction detected (PLIP) DMS.7: 3 residues within 4Å: Chain A: F.325, Q.326, P.349 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.326

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 6 residues within 4Å: Chain A: P.50, P.51, K.52, A.265, G.266, E.267 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.50, A:G.266 Water bridges: A:E.267

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bavetsias, V. et al., 8-Substituted Pyrido[3,4-d]pyrimidin-4(3H)-one Derivatives As Potent, Cell Permeable, KDM4 (JMJD2) and KDM5 (JARID1) Histone Lysine Demethylase Inhibitors. J.Med.Chem. (2016)

Release Date

2016-01-20

Peptides

Lysine-specific demethylase 4A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lysine-specific demethylase 4A

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