SMTL ID : 5f39.1 (3 other biounits)

Crystal structure of human KDM4A in complex with compound 37

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.65 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: 5UB.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: 5 residues within 4Å: Chain A: C.235, H.241, C.307, S.308, 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 5UB: 8-(1,3-thiazol-4-yl)-3~{H}-pyrido[3,4-d]pyrimidin-4-one(Non-covalent)

5UB.3: 12 residues within 4Å: Chain A: Y.133, Y.178, F.186, H.189, E.191, N.199, K.207, W.209, K.242, H.277 Ligands: ZN.1, DMS.5 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.186, A:W.209 Hydrogen bonds: A:Y.133, A:Y.133 Water bridges: A:N.199 pi-Stacking: A:F.186, A:H.189

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

DMS.4: 4 residues within 4Å: Chain A: Y.60, R.99, F.203, F.284 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.99 Salt bridges: A:D.64 pi-Cation interactions: A:F.203 DMS.5: 7 residues within 4Å: Chain A: G.171, Y.178, E.191, S.289, T.290, N.291 Ligands: 5UB.3 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:E.191 DMS.6: 6 residues within 4Å: Chain A: T.84, F.228, S.231, F.238, M.243, T.244 2 PLIP interactions: 2 interactions with chain A Water bridges: A:M.243 pi-Cation interactions: A:F.228 DMS.7: 4 residues within 4Å: Chain A: L.66, N.138, G.139, T.140 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.140

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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