SMTL ID : 4uf0.2 (1 other biounit)

Crystal structure of JmjC domain of human histone demethylase UTY in complex with epitherapuetic compound 2-(((2-((2-(dimethylamino)ethyl) (ethyl)amino)-2-oxoethyl)amino)methyl)isonicotinic acid.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

monomer

Ligands

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

FE2.1: 4 residues within 4Å: Chain A: H.217, E.219, H.297 Ligands: MMK.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.217, A:E.219, A:H.297, H2O.5

1 x MMK: 2-{[(2-{[(E)-2-(dimethylamino)ethenyl](ethyl)amino}-2-oxoethyl)amino]methyl}pyridine-4-carboxylic acid(Non-covalent)

MMK.2: 15 residues within 4Å: Chain A: F.155, Q.204, Y.206, K.208, T.214, H.217, E.219, N.220, N.227, W.237, H.297, V.299, N.307 Ligands: FE2.1, EDO.10 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.206, A:T.214, A:W.237, A:V.299 Hydrogen bonds: A:Y.206, A:N.227 Water bridges: A:T.214, A:S.225 Salt bridges: A:K.208

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: C.402, C.405, C.429, C.432 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.402, A:C.405, A:C.429, A:C.432

12 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 4 residues within 4Å: Chain A: V.247, D.250, F.251, A.274 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.250 Water bridges: A:D.270 EDO.5: 4 residues within 4Å: Chain A: Q.110, A.111, P.232, W.304 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.110 EDO.6: 3 residues within 4Å: Chain A: R.42, G.43, D.287 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.43, A:D.287 Water bridges: A:D.287 EDO.7: 4 residues within 4Å: Chain A: H.67, M.68, D.160 Ligands: EDO.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:M.68 Water bridges: A:E.66, A:K.166, A:K.166 EDO.8: 7 residues within 4Å: Chain A: H.67, M.68, E.70, N.158, I.159, D.160 Ligands: EDO.7 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:M.68, A:E.70, A:E.70, A:E.70, A:D.160 EDO.9: 8 residues within 4Å: Chain A: P.34, N.36, P.37, N.292, A.293, C.318, L.322 Ligands: EDO.15 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.36, A:N.292 EDO.10: 8 residues within 4Å: Chain A: G.199, Y.206, E.219, S.225, A.309, W.310, N.311 Ligands: MMK.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.206, A:N.311, A:N.311 Water bridges: A:S.225, A:S.225, A:S.225 EDO.11: 6 residues within 4Å: Chain A: H.195, I.197, P.338, P.340, A.399, Y.401 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:P.338, A:A.399, A:A.399 Water bridges: A:K.336 EDO.12: 5 residues within 4Å: Chain A: I.91, W.92, R.93, F.251, N.255 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:W.92, A:R.93 Water bridges: A:W.92, A:R.93, A:N.255 EDO.13: 5 residues within 4Å: Chain A: N.347, R.350, R.393, N.395, Y.449 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.350, A:R.393, A:R.393, A:N.395 Water bridges: A:N.347 EDO.14: 3 residues within 4Å: Chain A: T.376, E.379, A.380 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.376 EDO.15: 7 residues within 4Å: Chain A: T.32, P.34, N.292, A.293, T.316, C.318 Ligands: EDO.9 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.292, A:A.293, A:T.316, A:T.316

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Johansson, C. et al., Structural Analysis of Human Kdm5B Guides Histone Demethylase Inhibitor Development. Nat.Chem.Biol. (2016)

Release Date

2015-01-14

Peptides

HISTONE DEMETHYLASE UTY: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

HISTONE DEMETHYLASE UTY