SMTL ID : 5a7w.2 (1 other biounit)

Crystal structure of human JMJD2A in complex with compound 35

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.27 Å

Oligo State

monomer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: F.249, P.250, G.251, S.252 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.251, A:S.252

1 x 35M: 2-[5-[(4-hydroxyphenyl)carbonylamino]-2-oxidanyl-phenyl]pyridine-4-carboxylic acid(Non-covalent)

35M.2: 15 residues within 4Å: Chain A: I.93, N.108, Y.154, D.157, Y.199, F.207, H.210, E.212, N.220, K.228, W.230, K.263, H.298 Ligands: MN.3, DMS.8 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.207, A:W.230, A:K.263 Hydrogen bonds: A:N.220 Water bridges: A:N.108, A:S.218 Salt bridges: A:K.228 pi-Stacking: A:F.207 pi-Cation interactions: A:H.210

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

MN.3: 4 residues within 4Å: Chain A: H.210, E.212, H.298 Ligands: 35M.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.210, A:E.212, A:H.298, H2O.1

1 x ZN: ZINC ION(Non-covalent)

ZN.4: 5 residues within 4Å: Chain A: C.256, H.262, C.328, S.329, C.330 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.256, A:H.262, A:C.328, A:C.330

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

EDO.5: 7 residues within 4Å: Chain A: E.242, K.246, E.257, A.258, F.259, L.260, R.261 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.260, A:R.261 EDO.6: 6 residues within 4Å: Chain A: Y.133, F.136, P.227, T.283, E.285, H.303 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.285, A:E.285 EDO.7: 6 residues within 4Å: Chain A: T.105, F.249, S.252, H.262, M.264, T.265 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.105, A:S.252, A:H.262

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

DMS.8: 7 residues within 4Å: Chain A: G.192, Y.197, Y.199, E.212, S.310, N.312 Ligands: 35M.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.199, A:S.310 Salt bridges: A:E.212

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Korczynska, M. et al., Docking and Linking of Fragments to Discover Jumonji Histone Demethylase Inhibitors. J.Med.Chem. (2016)

Release Date

2016-01-13

Peptides

LYSINE-SPECIFIC DEMETHYLASE 4A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

LYSINE-SPECIFIC DEMETHYLASE 4A