SMTL ID : 5a7o.1 (1 other biounit)

Crystal structure of human JMJD2A in complex with compound 42

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 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 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.251, A:S.252 Water bridges: A:F.248, A:S.252

1 x 7WH: 2-[5-(2-methoxyethanoylamino)-2-oxidanyl-phenyl]pyridine-4-carboxylic acid(Non-covalent)

7WH.2: 14 residues within 4Å: Chain A: N.108, Y.154, Y.199, F.207, H.210, E.212, N.220, K.228, W.230, H.262, K.263, H.298 Ligands: MN.15, DMS.16 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.207, A:W.230, A:K.263 Hydrogen bonds: A:N.220 Water bridges: A:Q.106, A:N.108, A:D.157, A:D.157, A:A.208, A:S.310 Salt bridges: A:K.228 pi-Stacking: A:F.207 pi-Cation interactions: A:H.210

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

EDO.3: 5 residues within 4Å: Chain A: S.338, M.339, D.340, W.354, K.355 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:M.339, A:D.340, A:K.355 Water bridges: A:K.336, A:I.337, A:K.355 EDO.4: 8 residues within 4Å: Chain A: E.242, K.246, E.257, A.258, F.259, L.260, Y.297 Ligands: EDO.13 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.259, A:L.260 EDO.5: 2 residues within 4Å: Chain A: Y.81, R.120 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.120 EDO.6: 6 residues within 4Å: Chain A: T.98, G.99, L.103, F.104, T.105, F.249 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.105, A:T.105 EDO.7: 6 residues within 4Å: Chain A: D.215, K.239, Y.295, Q.324, V.326, H.365 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.239 Water bridges: A:V.326 EDO.8: 5 residues within 4Å: Chain A: Q.100, S.101, F.104, W.144, K.145 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.101 Water bridges: A:G.102, A:K.145, A:T.148 EDO.9: 3 residues within 4Å: Chain A: L.87, G.160, T.161 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.161 EDO.10: 4 residues within 4Å: Chain A: E.45, R.51, Y.55, F.375 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.45, A:R.51 EDO.11: 5 residues within 4Å: Chain A: I.188, I.190, M.334, V.335, K.336 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:M.334, A:K.336 Water bridges: A:K.336 EDO.12: 2 residues within 4Å: Chain A: K.111, K.112 No protein-ligand interaction detected (PLIP) EDO.13: 6 residues within 4Å: Chain A: H.210, T.211, L.260, R.261, Y.297 Ligands: EDO.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.211, A:T.211, A:Y.297, A:Y.297 Water bridges: A:R.261

1 x ZN: ZINC ION(Non-covalent)

ZN.14: 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

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

MN.15: 4 residues within 4Å: Chain A: H.210, E.212, H.298 Ligands: 7WH.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.210, A:E.212, A:H.298, H2O.4

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

DMS.16: 8 residues within 4Å: Chain A: G.192, Y.197, Y.199, E.212, S.218, S.310, T.311 Ligands: 7WH.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.199 Salt bridges: A:E.212

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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