SMTL ID : 5f5c.1

Crystal Structure of human JMJD2D complexed with KDOPP7

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.88 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: 5V3.11 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.196, A:E.198, A:H.284, H2O.1

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

EDO.3: 6 residues within 4Å: Chain A: A.87, G.88, W.130, S.254, T.256, V.257 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.254, A:S.254 EDO.4: 7 residues within 4Å: Chain A: F.35, K.154, Q.155, W.156, N.157, H.160, L.161 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.33, A:W.156, A:N.157, A:N.157 Water bridges: A:F.35 EDO.5: 4 residues within 4Å: Chain A: P.255, T.256, K.259, R.267 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.255, A:R.267, A:R.267 EDO.6: 5 residues within 4Å: Chain A: F.122, E.126, R.267, I.268, T.269 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:F.122, A:I.268, A:T.269 Water bridges: A:T.269, A:T.269 EDO.10: 6 residues within 4Å: Chain A: A.109, N.110, Q.115, T.116, G.290, F.291 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.116, A:F.291 Water bridges: A:T.116

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

SO4.7: 4 residues within 4Å: Chain A: R.64, E.65, T.66, N.69 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.65, A:T.66, A:T.66 Water bridges: A:T.66, A:N.69 Salt bridges: A:R.64 SO4.8: 3 residues within 4Å: Chain A: K.128, K.131, N.132 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.132 Salt bridges: A:K.128, A:K.131 SO4.9: 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, A:W.189 Water bridges: A:N.136 Salt bridges: A:K.190

1 x 5V3: 8-[[(phenylmethyl)amino]methyl]-1~{H}-pyrido[3,4-d]pyrimidin-4-one(Non-covalent)

5V3.11: 14 residues within 4Å: Chain A: Y.140, Y.183, Y.185, F.193, H.196, E.198, N.206, K.214, W.216, H.284, A.296, I.297, N.298 Ligands: NI.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.183, A:Y.185, A:W.216, A:A.296 Hydrogen bonds: A:Y.140, A:N.206 Water bridges: A:S.204 pi-Stacking: A:F.193

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

2015-12-30

Peptides

Lysine-specific demethylase 4D: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lysine-specific demethylase 4D

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