SMTL ID : 5f2s.1 (3 other biounits)

Crystal structure of human KDM4A in complex with compound 15

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.08 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: 5TZ.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 5TZ: 2-(2-azanyl-1,3-thiazol-4-yl)pyridine-4-carboxylic acid(Non-covalent)

5TZ.3: 11 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 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.186, A:W.209 Hydrogen bonds: A:E.191, A:N.199 Water bridges: A:D.192 Salt bridges: A:K.207 pi-Stacking: A:F.186, A:H.189

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:Y.178, A:S.289, A:T.290, A:N.291 Water bridges: A:S.197 EDO.5: 6 residues within 4Å: Chain A: T.84, F.228, S.231, F.238, M.243, T.244 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.83, A:S.231, A:S.231 Water bridges: A:T.244 EDO.6: 5 residues within 4Å: Chain A: E.119, R.120, W.123, P.248, L.249 No protein-ligand interaction detected (PLIP) EDO.7: 3 residues within 4Å: Chain A: L.66, G.139, T.140 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.140 EDO.8: 7 residues within 4Å: Chain A: I.151, G.152, R.153, L.154, T.290, N.291, F.292 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.152, A:L.154, A:N.291 Water bridges: A:R.155 EDO.9: 5 residues within 4Å: Chain A: N.10, P.11, S.12, A.13, R.14 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.10, A:S.12, A:A.13, A:R.14 EDO.10: 6 residues within 4Å: Chain A: S.12, A.13, R.14, P.213, F.258, D.259 2 PLIP interactions: 2 interactions with chain A Water bridges: A:A.13, A:D.259

2 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 Salt bridges: A:D.64 DMS.12: 3 residues within 4Å: Chain A: K.218, Y.274, Q.303 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.218 pi-Cation interactions: A:Y.274

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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