SMTL ID : 6dq6.2 (1 other biounit)

LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR N44 i.e. 3-((2-(pyridin-2-yl)-6-(4-(vinylsulfonyl)-1,4-diazepan-1-yl)pyrimidin-4-yl)amino)propanoic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.59 Å

Oligo State

homo-dimer

Ligands

2 x H6J: N-{6-[4-(ethenylsulfonyl)-1,4-diazepan-1-yl]-2-(pyridin-2-yl)pyrimidin-4-yl}-beta-alanine(Non-covalent)

H6J.1: 17 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, N.235, K.243, Q.277, L.278, A.323 Ligands: MN.2 8 PLIP interactions: 8 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, A:N.235 Salt bridges: A:K.243 H6J.5: 17 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, N.235, K.243, Q.277, L.278, A.323 Ligands: MN.6 8 PLIP interactions: 8 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, B:N.235 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: H6J.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 MN.6: 4 residues within 4Å: Chain B: H.225, E.227, H.313 Ligands: H6J.5 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.225, B:E.227, H2O.10, H2O.10

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 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 GOL.7: 4 residues within 4Å: Chain B: E.227, D.228, H.229, W.230 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.227, B:H.229 Water bridges: B:H.229

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.4: 3 residues within 4Å: Chain A: R.54, N.298, C.300 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.54, A:R.296, A:N.298 DMS.8: 3 residues within 4Å: Chain B: R.54, N.298, C.300 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.54, B:R.296, B:N.298

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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