SMTL ID : 5a80.1 (1 other biounit)

Crystal structure of human JMJD2A in complex with compound 40

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.28 Å

Oligo State

monomer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: F.249, P.250, G.251, S.252 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.251, A:S.252

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

MN.2: 4 residues within 4Å: Chain A: H.210, E.212, H.298 Ligands: 9CJ.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.210, A:E.212, A:H.298, H2O.2

1 x 9CJ: 2-[5-[2-(3-methoxyphenyl)ethanoylamino]-2-oxidanyl-phenyl]pyridine-4-carboxylic acid(Non-covalent)

9CJ.3: 14 residues within 4Å: Chain A: Y.154, D.157, Y.199, F.207, H.210, E.212, N.220, K.228, W.230, H.262, K.263, H.298 Ligands: MN.2, EDO.5 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.207, A:W.230 Hydrogen bonds: A:D.157, A:N.220 Water bridges: A:S.218, A:S.218, A:S.310 Salt bridges: A:K.228 pi-Stacking: A:F.207

1 x ZN: ZINC ION(Non-covalent)

ZN.4: 5 residues within 4Å: Chain A: C.256, H.262, C.328, S.329, C.330 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.256, A:H.262, A:C.328, A:C.330

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

EDO.5: 9 residues within 4Å: Chain A: G.192, Y.197, Y.199, E.212, S.218, S.310, T.311, N.312 Ligands: 9CJ.3 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.199, A:Y.199, A:S.218, A:S.310 Water bridges: A:S.218, A:S.218 EDO.6: 6 residues within 4Å: Chain A: H.210, T.211, L.260, R.261, Y.297, V.326 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.211, A:T.211, A:Y.297 Water bridges: A:R.261, A:R.261 EDO.7: 6 residues within 4Å: Chain A: K.246, A.253, C.256, E.257, A.258, F.259 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.253, A:F.259, A:L.260 EDO.8: 7 residues within 4Å: Chain A: I.172, G.173, R.174, L.175, N.194, N.312, F.313 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.173, A:L.175, A:N.312 Water bridges: A:R.176 EDO.9: 5 residues within 4Å: Chain A: I.337, S.338, M.339, D.340, W.354 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.339, A:D.340

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Korczynska, M. et al., Docking and Linking of Fragments to Discover Jumonji Histone Demethylase Inhibitors. J.Med.Chem. (2016)

Release Date

2016-01-13

Peptides

LYSINE-SPECIFIC DEMETHYLASE 4A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

LYSINE-SPECIFIC DEMETHYLASE 4A

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