SMTL ID : 5f5i.1 (1 other biounit)

Crystal Structure of human JMJD2A complexed with KDOOA011340

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.63 Å

Oligo State

monomer

Ligands

1 x NI: NICKEL (II) ION(Non-covalent)

NI.1: 4 residues within 4Å: Chain A: H.192, E.194, H.280 Ligands: 5V1.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.192, A:E.194, A:H.280, H2O.1

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.238, H.244, C.310, C.312 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.238, A:H.244, A:C.310, A:C.312

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 4 residues within 4Å: Chain A: F.231, P.232, G.233, S.234 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.233, A:S.234

1 x 5V1: 2-[[(phenylmethyl)amino]methyl]pyridine-4-carboxylic acid(Non-covalent)

5V1.4: 15 residues within 4Å: Chain A: Y.136, G.174, Y.179, Y.181, F.189, H.192, E.194, N.202, K.210, W.212, K.245, H.280, S.292, N.294 Ligands: NI.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.179, A:Y.181, A:F.189, A:W.212 Water bridges: A:S.200, A:S.292 Salt bridges: A:K.210 pi-Stacking: A:F.189

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

2015-12-30

Peptides

Lysine-specific demethylase 4A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lysine-specific demethylase 4A

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