SMTL ID : 6h4u.3 (3 other biounits)

Crystal structure of human KDM4A in complex with compound 34b

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.21 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: FO2.3 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 FO2: 8-[4-(1-methylpiperidin-4-yl)pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one(Non-covalent)

FO2.3: 14 residues within 4Å: Chain A: Y.133, G.171, Y.176, Y.178, F.186, H.189, E.191, D.192, N.199, K.207, W.209, K.242, H.277 Ligands: ZN.1 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.209, A:K.242 Hydrogen bonds: A:Y.133 Water bridges: A:S.197, A:S.289 pi-Stacking: A:F.186

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

DMS.4: 4 residues within 4Å: Chain A: L.223, G.226, F.227, Y.254 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:F.227 DMS.5: 4 residues within 4Å: Chain A: Y.112, F.115, T.262, H.282 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.262

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 1 residues within 4Å: Chain A: R.99 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Le Bihan, Y.V. et al., C8-substituted pyrido[3,4-d]pyrimidin-4(3H)-ones: Studies towards the identification of potent, cell penetrant Jumonji C domain containing histone lysine demethylase 4 subfamily (KDM4) inhibitors, compound profiling in cell-based target engagement assays. Eur.J.Med.Chem. (2019)

Release Date

2019-06-12

Peptides

Lysine-specific demethylase 4A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

Lysine-specific demethylase 4A

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