SMTL ID : 5a7n.2 (1 other biounit)

Crystal structure of human JMJD2A in complex with compound 43

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.39 Å

Oligo State

monomer

Ligands

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

MN.1: 4 residues within 4Å: Chain A: H.210, E.212, H.298 Ligands: VAO.6 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.210, A:E.212, A:H.298, H2O.4

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 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

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

EDO.3: 6 residues within 4Å: Chain A: G.192, Y.199, E.212, S.310, N.312 Ligands: VAO.6 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.199, A:Y.199, A:S.310, A:N.312, A:N.312 EDO.4: 5 residues within 4Å: Chain A: P.131, N.146, N.150, W.203, K.204 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.150

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

SO4.5: 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 VAO: 2-(5-cyano-2-oxidanyl-phenyl)pyridine-4-carboxylic acid(Non-covalent)

VAO.6: 11 residues within 4Å: Chain A: Y.154, F.207, H.210, E.212, N.220, K.228, W.230, K.263, H.298 Ligands: MN.1, EDO.3 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.207, A:W.230, A:K.263 Hydrogen bonds: A:N.220 Water bridges: A:S.218 Salt bridges: A:K.228 pi-Stacking: A:F.207 pi-Cation interactions: A:H.210

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

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