SMTL ID : 5f37.3 (3 other biounits)

Crystal structure of human KDM4A in complex with compound 58

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.22 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: N5J.3 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.189, A:E.191, A:H.277, H2O.2, H2O.3 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 N5J: 3H-pyrido[3,4-d]pyrimidin-4-one(Non-covalent)

N5J.3: 11 residues within 4Å: Chain A: Y.133, Y.178, F.186, H.189, N.199, K.207, W.209, K.242, H.277 Ligands: ZN.1, EDO.10 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.209 Hydrogen bonds: A:Y.133, A:Y.133, A:N.199, A:K.242 Water bridges: A:S.289 pi-Stacking: A:F.186

7 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 7 residues within 4Å: Chain A: G.171, Y.178, E.191, S.197, S.289, T.290, N.291 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.178, A:E.191, A:S.289 Water bridges: A:D.192, A:S.197, A:S.197 EDO.5: 6 residues within 4Å: Chain A: T.84, F.228, S.231, H.241, M.243, T.244 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.231, A:H.241 EDO.6: 2 residues within 4Å: Chain A: G.139, T.140 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.140 EDO.7: 6 residues within 4Å: Chain A: S.12, A.13, R.14, P.213, F.258, D.259 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.14 Water bridges: A:S.211, A:D.259 EDO.8: 2 residues within 4Å: Chain A: E.24, Y.31 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.24 EDO.9: 8 residues within 4Å: Chain A: I.151, G.152, R.153, L.154, D.159, N.173, N.291, F.292 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.152, A:L.154, A:N.291 EDO.10: 8 residues within 4Å: Chain A: I.72, Y.133, A.135, D.136, Y.178, S.185, K.242 Ligands: N5J.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.136, A:S.185, A:K.242 Water bridges: A:N.87

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

DMS.11: 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 pi-Cation interactions: A:F.203

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
C

Lysine-specific demethylase 4A

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