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

Crystal structure of human KDM4A in complex with compound 15

Coordinates

PDB Format Compare

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.4 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: 12 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, EDO.4 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

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

EDO.4: 9 residues within 4Å: Chain A: G.171, Y.176, Y.178, E.191, S.197, S.289, T.290, N.291 Ligands: 5TZ.3 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.178, A:Y.178, A:E.191, A:S.289, 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 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.244 EDO.6: 5 residues within 4Å: Chain A: E.119, R.120, W.123, P.248, L.249 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.120, A:W.123 EDO.7: 3 residues within 4Å: Chain A: L.66, G.139, T.140 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.140 Water bridges: A:R.57 EDO.8: 6 residues within 4Å: Chain A: S.12, A.13, R.14, P.213, F.258, D.259 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.14 Water bridges: A:S.211, A:F.258, A:D.259 EDO.9: 4 residues within 4Å: Chain A: E.24, Y.31, Y.34, F.354 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.24 Water bridges: A:E.24 EDO.10: 5 residues within 4Å: Chain A: K.106, Y.107, C.108, P.110, W.182 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.107 Water bridges: A:N.129 EDO.11: 9 residues within 4Å: Chain A: I.151, G.152, R.153, L.154, D.159, N.173, T.290, N.291, F.292 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.152, A:L.154, A:N.291 Water bridges: A:T.156, A:T.290 EDO.12: 5 residues within 4Å: Chain A: E.299, T.340, V.341, I.342, D.343 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.343, A:D.343

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

DMS.13: 5 residues within 4Å: Chain A: Y.60, D.64, R.99, F.203, F.284 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.99 Water bridges: A:D.64

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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