SMTL ID : 4ai9.2 (1 other biounit)

JMJD2A Complexed with Daminozide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

monomer

Ligands

1 x NI: NICKEL (II) ION(Non-covalent)

NI.1: 4 residues within 4Å: Chain A: H.210, E.212, H.298 Ligands: DZA.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.210, A:E.212, A:H.298, H2O.7

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

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

CL.3: 4 residues within 4Å: Chain A: F.249, P.250, G.251, S.252 Ligand excluded by PLIP

1 x DZA: DAMINOZIDE

DZA.4: 11 residues within 4Å: Chain A: Y.154, Y.199, F.207, H.210, E.212, S.218, N.220, K.228, K.263, H.298 Ligands: NI.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.207 Hydrogen bonds: A:Y.199, A:N.220 Water bridges: A:Y.199, A:Y.199 Salt bridges: A:E.212, A:K.228

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 4 residues within 4Å: Chain A: R.316, F.346, Q.347, P.370 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.316, A:Q.347 Water bridges: A:R.316

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rose, N.R. et al., Plant growth regulator daminozide is a selective inhibitor of human KDM2/7 histone demethylases. J. Med. Chem. (2012)

Release Date

2012-10-03

Peptides

LYSINE-SPECIFIC DEMETHYLASE 4A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

LYSINE-SPECIFIC DEMETHYLASE 4A

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