SMTL ID : 5f37.1 (3 other biounits)

Crystal structure of human KDM4A in complex with compound 58

Coordinates

PDB Format

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.1, 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 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 8 PLIP interactions: 8 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, A:F.186

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

EDO.4: 7 residues within 4Å: Chain A: G.171, Y.176, Y.178, E.191, S.289, T.290, N.291 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.289 Water bridges: A:E.191, A:S.197, A:S.197, A:I.198 EDO.5: 7 residues within 4Å: Chain A: T.84, F.228, S.231, F.238, H.241, M.243, T.244 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.231, A:H.241 EDO.6: 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.7: 8 residues within 4Å: Chain A: I.151, G.152, R.153, L.154, N.173, T.290, N.291, F.292 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.152, A:L.154, A:N.291 EDO.8: 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.9: 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, A:R.14 Water bridges: A:S.211, A:D.259 EDO.10: 10 residues within 4Å: Chain A: I.72, Q.74, N.87, Y.133, A.135, D.136, Y.178, S.185, K.242 Ligands: N5J.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.74, A:N.87, A:D.136, A:S.185, A:K.242 EDO.11: 6 residues within 4Å: Chain A: P.50, P.51, K.52, W.54, Y.200 Ligands: EDO.15 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.51, A:Y.200, A:Y.200 EDO.12: 6 residues within 4Å: Chain A: K.225, E.236, A.237, F.238, L.239, Y.276 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.238, A:L.239, A:Y.276 EDO.13: 6 residues within 4Å: Chain A: L.251, K.252, G.255, I.256, F.258 Ligands: EDO.14 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.251 EDO.14: 3 residues within 4Å: Chain A: P.257, F.258 Ligands: EDO.13 No protein-ligand interaction detected (PLIP) EDO.15: 4 residues within 4Å: Chain A: H.202, A.265, G.266 Ligands: EDO.11 No protein-ligand interaction detected (PLIP)

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

DMS.16: 4 residues within 4Å: Chain A: Y.60, 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.17: 7 residues within 4Å: Chain A: K.55, P.56, R.57, A.58, E.143, H.145, V.146 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:E.143

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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