SMTL ID : 6dq7.1

LINKED KDM5A JMJ DOMAIN BOUND TO THE POTENTIAL HYDROLYSIS PRODUCT OF INHIBITOR N45 i.e. 3-((6-(4-(2-cyano-3-methylbut-2-enoyl)-1,4-diazepan-1-yl)-2-(pyridin-2-yl)pyrimidin-4-yl)amino)propanoic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

monomer

Ligands

1 x H6M: N-{6-[4-(hydroxyacetyl)-1,4-diazepan-1-yl]-2-(pyridin-2-yl)pyrimidin-4-yl}-beta-alanine(Non-covalent)

H6M.1: 17 residues within 4Å: Chain A: R.75, Q.77, Y.151, A.153, D.154, Y.214, S.221, F.222, C.223, H.225, E.227, D.228, N.235, K.243, Q.277, A.323 Ligands: MN.2 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.214, A:Y.214, A:F.222 Hydrogen bonds: A:Y.151, A:C.223, A:N.235, A:Q.277 Water bridges: A:Y.214 Salt bridges: A:K.243

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

MN.2: 4 residues within 4Å: Chain A: H.225, E.227, H.313 Ligands: H6M.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.225, A:E.227, H2O.1, H2O.1

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 4 residues within 4Å: Chain A: K.52, R.54, N.298, C.300 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:K.52, A:K.52, A:R.54, A:N.298 Water bridges: A:T.129, A:T.129, A:T.129, A:T.129, A:R.296, A:N.298

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: E.227, D.228, H.229, W.230 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.227, A:D.228, A:H.229

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Horton, J.R. et al., Structure-based Engineering of Reversible Covalent Inhibitors Against Histone Lysine Demethylase 5A. To Be Published

Release Date

2019-06-12

Peptides

Linked KDM5A Jmj Domain: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Linked KDM5A Jmj Domain

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