SMTL ID : 5fp3.2 (1 other biounit)

Cell penetrant inhibitors of the JMJD2 (KDM4) and JARID1 (KDM5) families of histone lysine demethylases

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

monomer

Ligands

1 x YC8: 3-(4-phenylbutanoylamino)pyridine-4-carboxylic acid(Non-covalent)

YC8.1: 19 residues within 4Å: Chain A: R.107, Q.109, S.131, F.189, T.191, Y.240, K.242, R.247, T.248, P.249, H.251, N.261, W.271, H.331, V.333, N.341 Ligands: BCN.4, BCN.5, CO.7 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:R.107, A:F.189, A:F.189, A:T.191, A:Y.240, A:T.248, A:P.249, A:W.271, A:V.333 Hydrogen bonds: A:N.261 Water bridges: A:T.248, A:S.259 Salt bridges: A:K.242

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.436, C.439, C.463, C.466 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.436, A:C.439, A:C.463, A:C.466

2 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.3: 2 residues within 4Å: Chain A: E.276, E.359 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.276, H2O.9, H2O.14, H2O.14, H2O.14 MG.6: 2 residues within 4Å: Ligands: BCN.4, BCN.5 No protein-ligand interaction detected (PLIP)

2 x BCN: BICINE(Non-covalent)

BCN.4: 8 residues within 4Å: Chain A: R.107, P.249, H.251, T.295, G.296 Ligands: YC8.1, BCN.5, MG.6 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.107 BCN.5: 7 residues within 4Å: Chain A: H.251, Q.252, N.254, I.372 Ligands: YC8.1, BCN.4, MG.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.254

1 x CO: COBALT (II) ION(Non-covalent)

CO.7: 4 residues within 4Å: Chain A: H.251, E.253, H.331 Ligands: YC8.1 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.251, A:E.253, A:H.331, H2O.1, H2O.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Westaway, S.M. et al., Cell Penetrant Inhibitors of the Kdm4 and Kdm5 Families of Histone Lysine Demethylases. 1. 3-Amino-4-Pyridine Carboxylate Derivatives. J.Med.Chem. (2016)

Release Date

2016-01-27

Peptides

HUMAN LYSINE-SPECIFIC DEMETHYLASE 6B, JMJD3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

HUMAN LYSINE-SPECIFIC DEMETHYLASE 6B, JMJD3

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