SMTL ID : 5f5a.1

Crystal Structure of human JMJD2D complexed with KDOAM16

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.41 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.242, H.248, C.314, C.316 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.242, A:H.248, A:C.314, A:C.316

1 x NI: NICKEL (II) ION(Non-covalent)

NI.2: 4 residues within 4Å: Chain A: H.196, E.198, H.284 Ligands: 5V0.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.196, A:E.198, A:H.284, H2O.2

1 x 5V0: 2-[(furan-2-ylmethylamino)methyl]pyridine-4-carboxylic acid(Non-covalent)

5V0.3: 15 residues within 4Å: Chain A: Y.140, Y.183, Y.185, F.193, H.196, E.198, S.204, N.206, K.214, W.216, H.284, A.296, I.297, N.298 Ligands: NI.2 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.216 Hydrogen bonds: A:Y.140, A:N.206 Water bridges: A:S.204 Salt bridges: A:K.214 pi-Stacking: A:F.193

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

EDO.4: 7 residues within 4Å: Chain A: E.228, R.232, G.243, A.244, F.245, L.246, Y.283 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.232, A:L.246 Water bridges: A:A.244, A:R.247 EDO.5: 4 residues within 4Å: Chain A: E.31, K.37, Y.38, Y.41 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.31 EDO.6: 6 residues within 4Å: Chain A: F.35, K.154, Q.155, W.156, N.157, L.161 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.154, A:W.156, A:N.157 Water bridges: A:F.35 EDO.7: 5 residues within 4Å: Chain A: K.54, I.268, T.269, E.271 Ligands: EDO.15 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.54, A:K.54, A:T.269, A:T.269, A:T.269 EDO.8: 6 residues within 4Å: Chain A: A.87, G.88, W.130, K.131, S.254, T.256 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.130, A:S.254, A:T.256 Water bridges: A:T.256 EDO.9: 2 residues within 4Å: Chain A: H.107, N.110 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.107, A:N.110 EDO.10: 4 residues within 4Å: Chain A: P.255, T.256, K.259, R.267 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:P.255, A:R.267, A:R.267 Water bridges: A:T.256 EDO.11: 3 residues within 4Å: Chain A: M.23, I.24, F.25 2 PLIP interactions: 2 interactions with chain A Water bridges: A:I.24, A:I.24 EDO.12: 2 residues within 4Å: Chain A: F.265, R.267 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.259, A:F.265, A:R.267 Water bridges: A:F.265 EDO.13: 5 residues within 4Å: Chain A: F.25, H.26, E.31, Y.38, Y.41 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.26 Water bridges: A:H.26, A:T.28 EDO.14: 6 residues within 4Å: Chain A: S.84, G.85, V.89, F.90, T.91, F.235 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.89 EDO.15: 7 residues within 4Å: Chain A: F.122, E.126, T.215, R.267, I.268, T.269 Ligands: EDO.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.122, A:T.215, A:T.269 EDO.16: 3 residues within 4Å: Chain A: G.262, I.263, P.264 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.263 Water bridges: A:R.226

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

SO4.17: 4 residues within 4Å: Chain A: R.64, E.65, T.66, N.69 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.65, A:T.66, A:T.66, A:N.69 Water bridges: A:R.64, A:T.66 Salt bridges: A:R.64 SO4.18: 4 residues within 4Å: Chain A: R.127, K.128, K.131, N.132 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.132, A:N.132 Salt bridges: A:R.127, A:K.128, A:K.131 SO4.19: 5 residues within 4Å: Chain A: P.117, K.128, N.132, W.189, K.190 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.132 Water bridges: A:K.190, A:K.190 Salt bridges: A:K.190 SO4.20: 3 residues within 4Å: Chain A: D.306, Y.307, M.310 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bavetsias, V. et al., 8-Substituted Pyrido[3,4-d]pyrimidin-4(3H)-one Derivatives As Potent, Cell Permeable, KDM4 (JMJD2) and KDM5 (JARID1) Histone Lysine Demethylase Inhibitors. J.Med.Chem. (2016)

Release Date

2015-12-16

Peptides

Lysine-specific demethylase 4D: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lysine-specific demethylase 4D

Related Entries With Identical Sequence