SMTL ID : 6g8f.1

Crystal structure of UTX complexed with GSK-J1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.04 Å

Oligo State

monomer

Ligands

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

MN.1: 4 residues within 4Å: Chain A: H.276, E.278, H.356 Ligands: K0I.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.276, A:E.278, H2O.1, H2O.4

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 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

1 x K0I: 3-[[2-pyridin-2-yl-6-(1,2,4,5-tetrahydro-3-benzazepin-3-yl)pyrimidin-4-yl]amino]propanoic acid(Non-covalent)

K0I.3: 19 residues within 4Å: Chain A: R.131, Q.133, S.155, F.214, T.216, N.217, Y.265, K.267, R.272, T.273, P.274, H.276, E.278, N.279, N.286, V.358, N.366 Ligands: MN.1, DMS.7 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:R.131, A:F.214, A:Y.265, A:P.274 Hydrogen bonds: A:T.273, A:N.286 Water bridges: A:T.273 Salt bridges: A:K.267

4 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.4: 5 residues within 4Å: Chain A: V.243, A.245, S.250, H.251, N.410 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:H.251 DMS.5: 3 residues within 4Å: Chain A: F.82, A.238, R.241 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.238 DMS.6: 1 residues within 4Å: Chain A: R.157 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.157 DMS.7: 7 residues within 4Å: Chain A: P.274, G.275, H.276, L.319, M.320, G.321 Ligands: K0I.3 No protein-ligand interaction detected (PLIP)

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

CL.8: 3 residues within 4Å: Chain A: R.241, S.244, A.245 Ligand excluded by 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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