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

inhibitors of JumonjiC domain-containing histone demethylases

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x 5YQ: 2-{2-[(pyridin-3-ylmethyl)amino]pyrimidin-4-yl}pyridine-4-carboxylic acid(Non-covalent)

5YQ.1: 16 residues within 4Å: Chain A: Y.132, E.169, G.170, V.171, Y.175, Y.177, F.185, H.188, E.190, D.191, N.198, K.206, W.208, K.241, H.276 Ligands: FE2.2 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:V.171, A:F.185, A:F.185, A:F.185, A:W.208 Hydrogen bonds: A:E.190, A:N.198 Water bridges: A:Y.177, A:S.288, A:S.288, A:N.290 Salt bridges: A:K.206 pi-Stacking: A:H.188

1 x FE2: FE (II) ION(Non-covalent)

FE2.2: 4 residues within 4Å: Chain A: H.188, E.190, H.276 Ligands: 5YQ.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.188, A:E.190, A:H.276, H2O.5

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

SO4.3: 4 residues within 4Å: Chain A: F.227, P.228, G.229, S.230 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.227, A:G.229, A:S.230 SO4.4: 2 residues within 4Å: Chain A: K.89, K.90 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.90 Salt bridges: A:K.89, A:K.90

1 x ZN: ZINC ION(Non-covalent)

ZN.5: 4 residues within 4Å: Chain A: C.234, H.240, C.306, C.308 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.234, A:H.240, A:C.306, A:C.308

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

CL.6: 3 residues within 4Å: Chain A: S.316, M.317, W.332 Ligand excluded by PLIP CL.7: 1 residues within 4Å: Chain A: R.41 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain A: R.98, K.99, N.102 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Roatsch, M. et al., Substituted 2-(2-Aminopyrimidin-4-Yl)Pyridine-4-Carboxylates as Potent Inhibitors of Jumonjic Domain-Containing Histone Demethylases. Fut.Med.Chem. (2016)

Release Date

2016-03-23

Peptides

LYSINE-SPECIFIC DEMETHYLASE 4A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

LYSINE-SPECIFIC DEMETHYLASE 4A

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