- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.00 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x ZN: ZINC ION(Non-covalent)
- 2 x FE2: FE (II) ION(Non-covalent)
FE2.2: 4 residues within 4Å:- Chain A: H.185, E.187, H.273
- Ligands: YC8.6
5 PLIP interactions:3 interactions with chain A, 2 Ligand-Water interactions- Metal complexes: A:H.185, A:E.187, A:H.273, H2O.12, H2O.13
FE2.15: 4 residues within 4Å:- Chain B: H.185, E.187, H.273
- Ligands: YC8.19
5 PLIP interactions:3 interactions with chain B, 2 Ligand-Water interactions- Metal complexes: B:H.185, B:E.187, B:H.273, H2O.30, H2O.30
- 6 x GOL: GLYCEROL(Non-functional Binders)
GOL.3: 6 residues within 4Å:- Chain A: F.14, H.15, P.16, E.20, Y.27, Y.30
7 PLIP interactions:7 interactions with chain A- Hydrogen bonds: A:H.15, A:E.20, A:Y.27, A:Y.27
- Water bridges: A:H.15, A:H.15, A:T.17
GOL.4: 8 residues within 4Å:- Chain A: N.22, F.24, K.143, Q.144, W.145, N.146, H.149, L.150
7 PLIP interactions:7 interactions with chain A- Hydrogen bonds: A:F.24, A:W.145, A:N.146
- Water bridges: A:D.23, A:D.25, A:T.142, A:K.143
GOL.5: 4 residues within 4Å:- Chain A: F.111, R.256, I.257, T.258
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:T.258
- Water bridges: A:K.43
GOL.16: 6 residues within 4Å:- Chain B: F.14, H.15, P.16, E.20, Y.27, Y.30
5 PLIP interactions:5 interactions with chain B- Hydrogen bonds: B:H.15, B:E.20, B:Y.27, B:Y.27
- Water bridges: B:T.17
GOL.17: 8 residues within 4Å:- Chain B: N.22, F.24, K.143, Q.144, W.145, N.146, H.149, L.150
7 PLIP interactions:7 interactions with chain B- Hydrogen bonds: B:F.24, B:W.145, B:N.146
- Water bridges: B:D.23, B:D.25, B:T.142, B:K.143
GOL.18: 4 residues within 4Å:- Chain B: F.111, R.256, I.257, T.258
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:T.258, B:T.258
- Water bridges: B:K.43
- 2 x YC8: 3-(4-phenylbutanoylamino)pyridine-4-carboxylic acid(Non-covalent)
YC8.6: 13 residues within 4Å:- Chain A: L.68, H.83, Y.129, D.132, Y.174, F.182, H.185, N.195, K.203, W.205, K.238, H.273
- Ligands: FE2.2
11 PLIP interactions:11 interactions with chain A- Hydrophobic interactions: A:L.68, A:Y.129, A:Y.174, A:F.182, A:W.205, A:K.238
- Hydrogen bonds: A:N.195, A:K.238
- Salt bridges: A:K.203
- pi-Stacking: A:H.83, A:F.182
YC8.19: 13 residues within 4Å:- Chain B: L.68, H.83, Y.129, D.132, Y.174, F.182, H.185, N.195, K.203, W.205, K.238, H.273
- Ligands: FE2.15
12 PLIP interactions:12 interactions with chain B- Hydrophobic interactions: B:L.68, B:Y.129, B:Y.174, B:F.182, B:W.205, B:K.238
- Hydrogen bonds: B:Y.129, B:N.195, B:K.238
- Salt bridges: B:K.203
- pi-Stacking: B:H.83, B:F.182
- 14 x SO4: SULFATE ION(Non-functional Binders)
SO4.7: 5 residues within 4Å:- Chain A: P.106, K.117, N.121, W.178, K.179
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:N.121
- Water bridges: A:N.125, A:N.125, A:W.178
- Salt bridges: A:K.179
SO4.8: 4 residues within 4Å:- Chain A: R.53, E.54, T.55, N.58
7 PLIP interactions:7 interactions with chain A- Hydrogen bonds: A:E.54, A:T.55, A:N.58
- Water bridges: A:R.53, A:R.53, A:T.55
- Salt bridges: A:R.53
SO4.9: 4 residues within 4Å:- Chain A: R.116, K.117, K.120, N.121
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:N.121
- Salt bridges: A:R.116, A:K.117, A:K.120
SO4.10: 3 residues within 4Å:- Chain A: R.95, H.96, N.99
8 PLIP interactions:8 interactions with chain A- Hydrogen bonds: A:N.99
- Water bridges: A:R.95, A:H.96, A:H.96, A:H.96, A:H.96
- Salt bridges: A:R.95, A:H.96
SO4.11: 6 residues within 4Å:- Chain A: Y.172, Y.174, E.187, A.285, I.286, N.287
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:Y.174, A:Y.174, A:E.187
- Water bridges: A:N.287, A:N.287
SO4.12: 5 residues within 4Å:- Chain A: Q.109, N.110
- Chain B: Q.109, N.110
- Ligands: SO4.25
5 PLIP interactions:2 interactions with chain B, 3 interactions with chain A- Hydrogen bonds: B:Q.109, B:N.110, A:Q.109, A:Q.109, A:N.110
SO4.13: 3 residues within 4Å:- Chain A: D.295, Y.296, M.299
1 PLIP interactions:1 interactions with chain A- Water bridges: A:D.295
SO4.20: 5 residues within 4Å:- Chain B: P.106, K.117, N.121, W.178, K.179
5 PLIP interactions:5 interactions with chain B- Hydrogen bonds: B:N.121
- Water bridges: B:N.125, B:N.125, B:W.178
- Salt bridges: B:K.179
SO4.21: 4 residues within 4Å:- Chain B: R.53, E.54, T.55, N.58
7 PLIP interactions:7 interactions with chain B- Hydrogen bonds: B:E.54, B:T.55, B:N.58
- Water bridges: B:R.53, B:T.55, B:D.57
- Salt bridges: B:R.53
SO4.22: 4 residues within 4Å:- Chain B: R.116, K.117, K.120, N.121
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:N.121
- Salt bridges: B:R.116, B:K.117, B:K.120
SO4.23: 3 residues within 4Å:- Chain B: R.95, H.96, N.99
7 PLIP interactions:7 interactions with chain B- Hydrogen bonds: B:N.99
- Water bridges: B:R.95, B:H.96, B:H.96, B:H.96
- Salt bridges: B:R.95, B:H.96
SO4.24: 6 residues within 4Å:- Chain B: Y.172, Y.174, E.187, A.285, I.286, N.287
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:Y.174, B:E.187
- Water bridges: B:N.287, B:N.287
SO4.25: 5 residues within 4Å:- Chain A: Q.109, N.110
- Chain B: Q.109, N.110
- Ligands: SO4.12
5 PLIP interactions:3 interactions with chain B, 2 interactions with chain A- Hydrogen bonds: B:Q.109, B:Q.109, B:N.110, A:Q.109, A:N.110
SO4.26: 3 residues within 4Å:- Chain B: D.295, Y.296, M.299
No protein-ligand interaction detected (PLIP)- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Westaway, S.M. et al., Cell Penetrant Inhibitors of the Kdm4 and Kdm5 Families of Histone Lysine Demethylases. 1. 3-Amino-4-Pyridine Carboxylate Derivatives. J.Med.Chem. (2016)
- Release Date
- 2016-01-27
- Peptides
- LYSINE-SPECIFIC DEMETHYLASE 4D: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
A
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.00 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x ZN: ZINC ION(Non-covalent)
- 2 x FE2: FE (II) ION(Non-covalent)
- 6 x GOL: GLYCEROL(Non-functional Binders)
- 2 x YC8: 3-(4-phenylbutanoylamino)pyridine-4-carboxylic acid(Non-covalent)
- 14 x SO4: SULFATE ION(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Westaway, S.M. et al., Cell Penetrant Inhibitors of the Kdm4 and Kdm5 Families of Histone Lysine Demethylases. 1. 3-Amino-4-Pyridine Carboxylate Derivatives. J.Med.Chem. (2016)
- Release Date
- 2016-01-27
- Peptides
- LYSINE-SPECIFIC DEMETHYLASE 4D: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
A