SMTL ID : 6h4w.3 (3 other biounits)

Crystal structure of human KDM4A in complex with compound 19d

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.81 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: FQQ.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.189, A:E.191, A:H.277 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 FQQ: 8-[4-[2-[4-(3-chlorophenyl)-4-methyl-piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one(Non-covalent)

FQQ.3: 13 residues within 4Å: Chain A: Y.133, D.136, Y.176, Y.178, F.186, H.189, E.191, N.199, K.207, W.209, K.242, H.277 Ligands: ZN.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:D.136, A:Y.176, A:Y.176, A:W.209 Hydrogen bonds: A:Y.133, A:Y.133, A:K.242 Water bridges: A:S.289 Salt bridges: A:D.136, A:D.192 pi-Stacking: A:F.186

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

DMS.4: 4 residues within 4Å: Chain A: Y.60, R.99, F.203, F.284 No protein-ligand interaction detected (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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