SMTL ID : 5fpl.1

Crystal structure of human JARID1B in complex with CCT363901

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.400, C.403, C.423, H.426 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.400, A:C.403, A:C.423, A:H.426

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

MN.2: 5 residues within 4Å: Chain A: L.66, N.67, L.121, T.124, E.127 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:L.66, A:L.121, A:T.124, A:E.127 MN.3: 4 residues within 4Å: Chain A: H.207, E.209, H.295 Ligands: QAY.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.207, A:E.209, A:H.295, H2O.6

1 x QAY: 8-[4-(2-azanylethyl)pyrazol-1-yl]-3H-pyrido[3,4-d]pyrimidin-4-one(Non-covalent)

QAY.4: 12 residues within 4Å: Chain A: R.74, Y.133, D.136, Y.196, F.204, H.207, E.209, N.217, K.225, W.227, H.295 Ligands: MN.3 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.227 Hydrogen bonds: A:Y.133, A:Y.133, A:D.136, A:N.217 pi-Stacking: A:Y.196, A:F.204

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

EDO.5: 5 residues within 4Å: Chain A: D.338, C.407, F.408, M.409, S.410 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.338, A:F.408, A:M.409, A:S.410, A:S.410 EDO.6: 4 residues within 4Å: Chain A: G.232, Y.233, R.292, L.318 No protein-ligand interaction detected (PLIP)

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

DMS.7: 6 residues within 4Å: Chain A: I.208, W.212, R.292, H.325, Y.326, L.329 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bavetsias, V. et al., 8-Substituted Pyrido[3,4-D]Pyrimidin-4(3H)-One Derivatives as Potent, Cell Permeable, Kdm4 (Jmjd2) and Kdm5 (Jarid1) Histone Lysine Demethylase Inhibitors. J.Med.Chem. (2016)

Release Date

2016-01-20

Peptides

LYSINE-SPECIFIC DEMETHYLASE 5B, LYSINE-SPECIFIC DEMETHYLASE 5B: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

LYSINE-SPECIFIC DEMETHYLASE 5B, LYSINE-SPECIFIC DEMETHYLASE 5B