SMTL ID : 6cg2.2 (3 other biounits)

Crystal Structure of KDM4A with Compound 8

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.34 Å

Oligo State

monomer

Ligands

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

NI.1: 4 residues within 4Å: Chain A: H.184, E.186, H.272 Ligands: QC2.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.184, A:E.186, A:H.272, H2O.2

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: C.230, H.236, C.302, S.303, C.304 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.230, A:H.236, A:C.302, A:C.304

1 x QC2: 2-[5-(3-hydroxyphenyl)-1H-pyrazol-1-yl]pyridine-4-carboxylic acid(Non-covalent)

QC2.3: 12 residues within 4Å: Chain A: Y.128, D.131, Y.173, S.180, F.181, H.184, E.186, K.202, W.204, K.237, H.272 Ligands: NI.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.173, A:F.181, A:W.204, A:K.237 Water bridges: A:A.182 Salt bridges: A:K.202 pi-Stacking: A:F.181, A:H.184

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nie, Z. et al., Structure-based design and discovery of potent and selective KDM5 inhibitors. Bioorg. Med. Chem. Lett. (2018)

Release Date

2018-04-18

Peptides

Lysine-specific demethylase 4A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Lysine-specific demethylase 4A

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