SMTL ID : 5a7q.1 (1 other biounit)

Crystal structure of human JMJD2A in complex with compound 30

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

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

MN.1: 4 residues within 4Å: Chain A: H.210, E.212, H.298 Ligands: KCH.3 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 MN.2: 3 residues within 4Å: Chain A: F.249, G.251, S.252 No protein-ligand interaction detected (PLIP)

1 x KCH: 2-(5-azanyl-2-oxidanyl-phenyl)pyridine-4-carboxylic acid(Non-covalent)

KCH.3: 11 residues within 4Å: Chain A: Y.154, Y.199, F.207, H.210, E.212, N.220, K.228, W.230, K.263, H.298 Ligands: MN.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.207, A:W.230, A:K.263 Hydrogen bonds: A:Y.154, A:N.220 Water bridges: A:Y.199, A:S.218 Salt bridges: A:K.228 pi-Stacking: A:F.207, A:H.210

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

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 3 residues within 4Å: Chain A: A.258, F.259, L.260 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain A: G.192, Y.199, S.310 Ligand excluded by PLIP

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
A

LYSINE-SPECIFIC DEMETHYLASE 4A

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