SMTL ID : 3pdq.1 (1 other biounit)

Crystal structure of JMJD2A complexed with bipyridyl inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.99 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: KC6.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.210, A:E.212, A:H.298, H2O.6

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 KC6: 4'-[(2-aminoethyl)carbamoyl]-2,2'-bipyridine-4-carboxylic acid(Non-covalent)

KC6.3: 13 residues within 4Å: Chain A: Y.154, D.157, Y.197, Y.199, F.207, H.210, E.212, N.220, K.228, W.230, K.263, H.298 Ligands: NI.1 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.207, A:W.230, A:K.263 Hydrogen bonds: A:D.157, A:N.220 Water bridges: A:N.108, A:Y.199, A:S.310, A:N.312 Salt bridges: A:K.228 pi-Stacking: A:F.207, A:H.210

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

CL.4: 4 residues within 4Å: Chain A: F.249, P.250, G.251, S.252 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain A: Q.106, N.108, K.263, M.264 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain A: F.39, Y.40 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain A: R.261, L.327, C.328, V.335 Ligand excluded by PLIP

1 x NA: SODIUM ION(Non-functional Binders)

NA.7: 2 residues within 4Å: Chain A: E.191, Y.197 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.159, A:Y.197, A:Y.197

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chang, K.-H. et al., Inhibition of histone demethylases by 4-carboxy-2,2'-bipyridyl compounds. Chemmedchem (2011)

Release Date

2011-03-30

Peptides

Lysine-specific demethylase 4A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lysine-specific demethylase 4A

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