SMTL ID : 6dqc.1

LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR N50 i.e. 2-(4-((2-(dimethylamino)ethyl)(ethyl)carbamoyl)-5-(4-methoxyphenyl)-1H-pyrazol-1-yl)isonicotinic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

monomer

Ligands

1 x H5Y: 2-[4-{[2-(dimethylamino)ethyl](ethyl)carbamoyl}-5-(4-methoxyphenyl)-1H-pyrazol-1-yl]pyridine-4-carboxylic acid(Non-covalent)

H5Y.1: 15 residues within 4Å: Chain A: R.75, Q.77, Y.151, A.153, Y.214, S.221, F.222, H.225, E.227, D.228, K.243, W.245, H.313 Ligands: MN.2, DMS.3 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:A.153, A:Y.214, A:F.222, A:H.225, A:W.245 Hydrogen bonds: A:Y.151 Salt bridges: A:D.228, 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: H5Y.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.225, A:E.227, A:H.313, H2O.2

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

DMS.3: 7 residues within 4Å: Chain A: Y.214, E.227, S.233, A.325, V.326, N.327 Ligands: H5Y.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.214 Salt bridges: A:E.227

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 3 residues within 4Å: Chain A: E.20, N.298, C.300 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.20, A:N.298, A:N.298 Water bridges: A:R.54, A:R.296, A:N.298

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

SO4.5: 5 residues within 4Å: Chain A: C.65, E.66, V.67, K.68, R.171 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:C.65, A:V.67, A:K.68 Salt bridges: A:R.171

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Horton, J.R. et al., To be determined. 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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