SMTL ID : 5vmp.2 (3 other biounits)

Crystal Structure of Human KDM4 with Small Molecule Inhibitor QC5714

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.48 Å

Oligo State

monomer

Ligands

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

NI.1: 4 residues within 4Å: Chain A: H.203, E.205, H.291 Ligands: 9FJ.3 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.203, A:E.205, A:H.291, H2O.1, H2O.2

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.249, H.255, C.321, C.323 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.249, A:H.255, A:C.321, A:C.323

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

9FJ.3: 15 residues within 4Å: Chain A: I.86, Q.88, N.101, Y.147, Y.192, S.199, F.200, H.203, N.213, K.221, W.223, H.255, K.256, H.291 Ligands: NI.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.86, A:Y.147, A:W.223, A:K.256 Hydrogen bonds: A:N.213 Salt bridges: A:K.221 pi-Stacking: A:F.200

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
B

Lysine-specific demethylase 4A

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