SMTL ID : 6dqa.1

Linked KDM5A JMJ Domain Bound to Inhibitor N70 i.e.[2-((3-aminophenyl)(2-(piperidin-1-yl)ethoxy)methyl)thieno[3,2-b]pyridine-7-carboxylic acid]

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

monomer

Ligands

1 x H6V: 2-{(R)-(3-aminophenyl)[2-(piperidin-1-yl)ethoxy]methyl}thieno[3,2-b]pyridine-7-carboxylic acid(Non-covalent)

H6V.1: 15 residues within 4Å: Chain A: R.75, Q.77, Y.151, D.154, Y.214, S.221, F.222, C.223, H.225, N.235, K.243, W.245, H.313 Ligands: MN.2, GOL.4 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.222, A:W.245 Hydrogen bonds: A:Y.151, A:C.223 Water bridges: A:R.75, A:C.223, A:Q.277 Salt bridges: A:D.154, A:K.243 pi-Stacking: A:F.222 pi-Cation interactions: A:W.212, A:W.212

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

MN.2: 4 residues within 4Å: Chain A: H.225, E.227, H.313 Ligands: H6V.1 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.225, A:E.227, A:H.313, H2O.2, H2O.3

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: S.117, N.121, M.122, P.123 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.117, A:M.122 GOL.4: 7 residues within 4Å: Chain A: R.75, Q.77, E.81, S.221, C.223, L.278 Ligands: H6V.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.75, A:Q.77

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

EDO.5: 4 residues within 4Å: Chain A: S.141, I.281, M.282, N.283 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.283 Water bridges: A:E.83 EDO.6: 4 residues within 4Å: Chain A: R.42, Y.232, P.309, T.330 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.42, A:Y.232, A:T.330 EDO.7: 3 residues within 4Å: Chain A: F.15, P.17, E.130 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.15 Water bridges: A:E.130

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: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Linked KDM5A Jmj Domain

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