SMTL ID : 5f3i.4 (3 other biounits)

Crystal structure of human KDM4A in complex with compound 54j

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.24 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: 5UJ.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 5UJ: 8-[4-[2-[4-[3,5-bis(chloranyl)phenyl]piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one(Non-covalent)

5UJ.3: 12 residues within 4Å: Chain A: Y.133, D.136, Y.176, Y.178, F.186, H.189, E.191, K.207, W.209, K.242, H.277 Ligands: ZN.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.176, A:F.186, A:W.209, A:K.242 Hydrogen bonds: A:Y.133 Water bridges: A:S.289 Salt bridges: A:D.136, A:D.192 pi-Stacking: A:F.186

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

DMS.4: 5 residues within 4Å: Chain A: A.232, Q.233, C.235, E.236, S.308 No protein-ligand interaction detected (PLIP) DMS.5: 3 residues within 4Å: Chain A: K.252, P.257, F.258 No protein-ligand interaction detected (PLIP)

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
D

Lysine-specific demethylase 4A

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