- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.30 Å
- Oligo State
- monomer
- Ligands
- 2 x ZN: ZINC ION(Non-covalent)
- 3 x MN: MANGANESE (II) ION(Non-covalent)
MN.3: 4 residues within 4Å:- Chain A: H.208, E.210, H.296
- Ligands: FQ5.5
4 PLIP interactions:3 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:H.208, A:E.210, A:H.296, H2O.1
MN.4: 5 residues within 4Å:- Chain A: L.67, N.68, L.122, T.125, E.128
4 PLIP interactions:3 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:L.122, A:T.125, A:E.128, H2O.2
MN.22: 1 residues within 4Å:- Chain A: D.339
No protein-ligand interaction detected (PLIP)- 2 x FQ5: 8-[4-[2-[4-(3-chlorophenyl)piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one(Non-covalent)
FQ5.5: 16 residues within 4Å:- Chain A: R.75, Y.134, D.137, C.189, W.195, Y.197, F.205, H.208, E.210, N.218, K.226, W.228, H.296
- Ligands: MN.3, DMS.7, DMS.11
8 PLIP interactions:8 interactions with chain A- Hydrophobic interactions: A:D.137, A:W.195, A:W.228
- Hydrogen bonds: A:Y.134, A:Y.134, A:N.218
- Salt bridges: A:D.137
- pi-Stacking: A:F.205
FQ5.6: 7 residues within 4Å:- Chain A: E.8, P.10, I.32, Q.35, T.36, Y.234, Y.278
5 PLIP interactions:5 interactions with chain A- Hydrophobic interactions: A:P.10, A:T.36, A:Y.234
- Hydrogen bonds: A:Q.35
- pi-Stacking: A:Y.234
- 9 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)
DMS.7: 7 residues within 4Å:- Chain A: W.195, Y.197, E.210, S.216, A.308, N.310
- Ligands: FQ5.5
1 PLIP interactions:1 interactions with chain A- Salt bridges: A:E.210
DMS.8: 7 residues within 4Å:- Chain A: I.209, W.213, H.326, Y.327, L.330, R.332
- Ligands: EDO.21
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:H.326
- Water bridges: A:Y.327
- Salt bridges: A:E.240
DMS.9: 7 residues within 4Å:- Chain A: E.340, C.343, K.344, E.392, F.409, R.444, Y.445
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:Y.445
- Water bridges: A:R.444
- Salt bridges: A:E.392
DMS.10: 3 residues within 4Å:- Chain A: G.420, L.421, L.422
No protein-ligand interaction detected (PLIP)DMS.11: 7 residues within 4Å:- Chain A: R.75, F.205, C.206, H.208, V.262
- Ligands: FQ5.5, DMS.12
1 PLIP interactions:1 interactions with chain A- pi-Cation interactions: A:H.208
DMS.12: 7 residues within 4Å:- Chain A: Q.65, Q.73, T.74, S.204, F.205, C.206
- Ligands: DMS.11
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:Q.65, A:C.206
DMS.13: 5 residues within 4Å:- Chain A: R.375, S.386, L.441, Y.443, T.446
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:R.375
- pi-Cation interactions: A:Y.443
DMS.14: 4 residues within 4Å:- Chain A: E.430, L.431, C.432, S.433
No protein-ligand interaction detected (PLIP)DMS.15: 1 residues within 4Å:- Chain A: H.108
3 PLIP interactions:3 interactions with chain A- Water bridges: A:H.108
- Salt bridges: A:D.96
- pi-Cation interactions: A:H.108
- 6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.16: 5 residues within 4Å:- Chain A: D.339, C.408, F.409, M.410, S.411
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:D.339, A:F.409, A:M.410, A:S.411, A:S.411
EDO.17: 4 residues within 4Å:- Chain A: G.233, Y.234, R.293, L.319
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:R.293
- Water bridges: A:G.233
EDO.18: 3 residues within 4Å:- Chain A: H.331, K.403, H.427
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:H.331
EDO.19: 8 residues within 4Å:- Chain A: D.397, E.398, R.399, Q.400, V.402, G.420, L.421, L.422
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:D.397, A:Q.400, A:L.422, A:L.422
EDO.20: 3 residues within 4Å:- Chain A: M.2, L.4, N.268
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:N.268
EDO.21: 6 residues within 4Å:- Chain A: D.211, Q.260, Y.327, R.332, Y.333
- Ligands: DMS.8
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:D.211, A:R.332
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Le Bihan, Y.V. et al., C8-substituted pyrido[3,4-d]pyrimidin-4(3H)-ones: Studies towards the identification of potent, cell penetrant Jumonji C domain containing histone lysine demethylase 4 subfamily (KDM4) inhibitors, compound profiling in cell-based target engagement assays. Eur.J.Med.Chem. (2019)
- Release Date
- 2019-06-12
- Peptides
- Lysine-specific demethylase 5B,Lysine-specific demethylase 5B: A
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
A
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.30 Å
- Oligo State
- monomer
- Ligands
- 2 x ZN: ZINC ION(Non-covalent)
- 3 x MN: MANGANESE (II) ION(Non-covalent)
- 2 x FQ5: 8-[4-[2-[4-(3-chlorophenyl)piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one(Non-covalent)
- 9 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)
- 6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Le Bihan, Y.V. et al., C8-substituted pyrido[3,4-d]pyrimidin-4(3H)-ones: Studies towards the identification of potent, cell penetrant Jumonji C domain containing histone lysine demethylase 4 subfamily (KDM4) inhibitors, compound profiling in cell-based target engagement assays. Eur.J.Med.Chem. (2019)
- Release Date
- 2019-06-12
- Peptides
- Lysine-specific demethylase 5B,Lysine-specific demethylase 5B: A
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
A