SMTL ID : 6cg1.2 (3 other biounits)

Crystal Structure of KDM4A with Compound 14

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.16 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: QC1.3 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.184, A:E.186, A:H.272, H2O.2, 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 QC1: 3-{[(4-fluorophenyl)methyl]amino}pyridine-4-carboxylic acid(Non-covalent)

QC1.3: 14 residues within 4Å: Chain A: I.67, Q.69, Y.128, A.130, D.131, Y.173, S.180, F.181, H.184, N.194, K.202, W.204, H.272 Ligands: NI.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.128, A:Y.128, A:A.130, A:W.204 Hydrogen bonds: A:N.194 Salt bridges: A:K.202 pi-Stacking: A:F.181

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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