SMTL ID : 6dq5.2 (1 other biounit)

LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR N43 i.e. 3-((6-(4-acryloyl-1,4-diazepan-1-yl)-2-(pyridin-2-yl)pyrimidin-4-yl)amino)propanoic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

homo-dimer

Ligands

2 x H6G: N-[6-(4-acryloyl-1,4-diazepan-1-yl)-2-(pyridin-2-yl)pyrimidin-4-yl]-beta-alanine(Non-covalent)

H6G.1: 15 residues within 4Å: Chain A: R.75, Y.151, A.153, D.154, Y.214, S.221, F.222, C.223, H.225, E.227, D.228, K.243, Q.277, A.323 Ligands: MN.2 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.214, A:Y.214, A:F.222, A:H.225 Hydrogen bonds: A:Y.151, A:C.223 Salt bridges: A:K.243 H6G.3: 15 residues within 4Å: Chain B: R.75, Y.151, A.153, D.154, Y.214, S.221, F.222, C.223, H.225, E.227, D.228, K.243, Q.277, A.323 Ligands: MN.4 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:Y.214, B:Y.214, B:F.222, B:H.225 Hydrogen bonds: B:Y.151, B:C.223 Salt bridges: B:K.243

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 4 residues within 4Å: Chain A: H.225, E.227, H.313 Ligands: H6G.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.225, A:E.227, H2O.1, H2O.2 MN.4: 4 residues within 4Å: Chain B: H.225, E.227, H.313 Ligands: H6G.3 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.225, B:E.227, H2O.5, H2O.6

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Horton, J.R. et al., Structure-Based Engineering of Irreversible Inhibitors against Histone Lysine Demethylase KDM5A. J. Med. Chem. (2018)

Release Date

2018-11-21

Peptides

Linked KDM5A Jmj Domain: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Linked KDM5A Jmj Domain

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