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

Crystal Structure of KDM4 with the Small Molecule Inhibitor QC6352

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.07 Å

Oligo State

monomer

Ligands

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

NI.1: 4 residues within 4Å: Chain A: H.204, E.206, H.292 Ligands: 9DJ.3 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.204, A:E.206, A:H.292, H2O.1, H2O.1

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: C.250, H.256, C.322, S.323, C.324 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.250, A:H.256, A:C.322, A:C.324

1 x 9DJ: 3-[({(1R)-6-[methyl(phenyl)amino]-1,2,3,4-tetrahydronaphthalen-1-yl}methyl)amino]pyridine-4-carboxylic acid(Non-covalent)

9DJ.3: 18 residues within 4Å: Chain A: I.87, Q.89, N.102, Y.148, D.151, Y.193, S.200, F.201, H.204, N.214, K.222, W.224, R.255, H.256, K.257, H.292, R.325 Ligands: NI.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:I.87, A:Y.148, A:Y.148, A:W.224, A:K.257 Hydrogen bonds: A:Y.148, A:N.214 Salt bridges: A:K.222 pi-Stacking: A:F.201

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, Y.K. et al., Design of KDM4 Inhibitors with Antiproliferative Effects in Cancer Models. ACS Med Chem Lett (2017)

Release Date

2017-09-27

Peptides

Lysine-specific demethylase 4A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

Lysine-specific demethylase 4A

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