SMTL ID : 6bgu.1

LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR 2-((2-chlorophenyl)(propoxy)methyl)-1H-pyrrolo[3,2-b]pyridine (Compound N9)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.68 Å

Oligo State

monomer

Ligands

1 x DKP: 2-[(R)-(2-chlorophenyl)(propoxy)methyl]-1H-pyrrolo[3,2-b]pyridine-7-carboxylic acid(Non-covalent)

DKP.1: 15 residues within 4Å: Chain A: R.75, Q.77, Y.151, A.153, Y.214, S.221, F.222, C.223, H.225, N.235, K.243, W.245, Q.277, H.313 Ligands: MN.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.151, A:A.153, A:H.225, A:W.245 Hydrogen bonds: A:Y.151 Water bridges: A:C.223, A:N.235 Salt bridges: A:K.243 pi-Stacking: A:F.222, A:H.225

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

MN.2: 4 residues within 4Å: Chain A: H.225, E.227, H.313 Ligands: DKP.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.5

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

DMS.3: 7 residues within 4Å: Chain A: L.256, E.257, M.260, D.273, H.276, T.280, Y.312 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:D.273

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: W.230, S.250, P.309, R.310 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.250, A:R.310 Water bridges: A:S.250, A:P.309 GOL.5: 12 residues within 4Å: Chain A: F.136, W.137, S.221, F.222, C.223, W.224, T.280, I.281, M.282, S.314, G.315, F.316 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.221, A:W.224, A:M.282, A:M.282, A:S.314, A:G.315

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

EDO.6: 2 residues within 4Å: Chain A: E.257, R.310 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.257, A:R.310 EDO.7: 2 residues within 4Å: Chain A: M.122, P.123 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.122 EDO.8: 4 residues within 4Å: Chain A: E.66, V.67, K.68, R.171 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.67, A:K.68, A:R.171 EDO.9: 3 residues within 4Å: Chain A: E.25, P.55, K.57 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.25, A:P.55

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.10: 6 residues within 4Å: Chain A: Q.77, R.78, L.79, E.81, S.221, I.281 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.78, A:E.81, A:S.221, A:S.221 Water bridges: A:Q.77, A:E.81

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Horton, J.R. et al., Insights into the Action of Inhibitor Enantiomers against Histone Lysine Demethylase 5A. J. Med. Chem. (2018)

Release Date

2018-03-28

Peptides

Lysine-specific demethylase 5A, linked KDM5A JMJ domain: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lysine-specific demethylase 5A, linked KDM5A JMJ domain

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