SMTL ID : 6ful.1

Crystal structure of UTX complexed with 5-hydroxy-4-keto-1-methyl-picolinate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

monomer

Ligands

1 x E7Z: 1-methyl-5-oxidanyl-4-oxidanylidene-pyridine-2-carboxylic acid(Non-covalent)

E7Z.1: 10 residues within 4Å: Chain A: Y.265, K.267, T.273, H.276, E.278, N.286, H.356, V.358, N.366 Ligands: MN.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:T.273, A:V.358 Hydrogen bonds: A:T.273, A:T.273, A:N.286 Water bridges: A:T.273, A:S.284 Salt bridges: A:K.267

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

MN.2: 4 residues within 4Å: Chain A: H.276, E.278, H.356 Ligands: E7Z.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.276, A:E.278, A:H.356, H2O.7

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: C.461, C.464, C.488, C.491 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.461, A:C.464, A:C.488, A:C.491

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

SO4.4: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.28 SO4.5: 4 residues within 4Å: Chain A: F.82, P.237, A.238, R.241 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:A.238 Water bridges: A:F.239, A:R.241, A:R.241, A:R.241 Salt bridges: A:R.241 SO4.6: 4 residues within 4Å: Chain A: Y.379, K.380, V.383, M.421 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.380 SO4.7: 4 residues within 4Å: Chain A: N.77, K.78, A.106, K.108 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:K.78 Water bridges: A:R.79, A:R.79, A:K.108, A:K.108, A:K.108, A:K.108 Salt bridges: A:K.108 SO4.8: 5 residues within 4Å: Chain A: R.452, T.453, K.454, E.455, E.456 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:E.455, A:E.456 Water bridges: A:N.406, A:R.452, A:R.452, A:R.452, A:R.452 Salt bridges: A:R.452 SO4.9: 5 residues within 4Å: Chain A: R.241, S.244, A.245, G.246 Ligands: PG0.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.241, A:G.246

1 x PG0: 2-(2-METHOXYETHOXY)ETHANOL(Non-functional Binders)

PG0.10: 7 residues within 4Å: Chain A: V.243, S.244, A.245, S.250, H.251, N.410 Ligands: SO4.9 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Esposito, C. et al., In Silico Identification of JMJD3 Demethylase Inhibitors. J Chem Inf Model (2018)

Release Date

2018-10-10

Peptides

Lysine-specific demethylase 6A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lysine-specific demethylase 6A

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