- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.72 Å
- Oligo State
- homo-trimer
- Ligands
- 3 x ZN: ZINC ION(Non-covalent)
- 6 x CA: CALCIUM ION(Non-covalent)
CA.2: 6 residues within 4Å:- Chain A: D.169, D.171, H.173, S.192, F.193, H.194
5 PLIP interactions:5 interactions with chain A- Metal complexes: A:D.169, A:D.169, A:D.171, A:H.173, A:F.193
CA.3: 4 residues within 4Å:- Chain A: F.182, T.185, V.188, Y.217
5 PLIP interactions:3 interactions with chain A, 2 Ligand-Water interactions- Metal complexes: A:F.182, A:T.185, A:V.188, H2O.3, H2O.3
CA.12: 6 residues within 4Å:- Chain B: D.169, D.171, H.173, S.192, F.193, H.194
5 PLIP interactions:5 interactions with chain B- Metal complexes: B:D.169, B:D.169, B:D.171, B:H.173, B:S.192
CA.13: 4 residues within 4Å:- Chain B: F.182, T.185, V.188, Y.217
5 PLIP interactions:3 interactions with chain B, 2 Ligand-Water interactions- Metal complexes: B:F.182, B:T.185, B:V.188, H2O.15, H2O.15
CA.26: 6 residues within 4Å:- Chain C: D.169, D.171, H.173, S.192, F.193, H.194
5 PLIP interactions:5 interactions with chain C- Metal complexes: C:D.169, C:D.171, C:H.173, C:S.192, C:F.193
CA.27: 4 residues within 4Å:- Chain C: F.182, T.185, V.188, Y.217
5 PLIP interactions:3 interactions with chain C, 2 Ligand-Water interactions- Metal complexes: C:F.182, C:T.185, C:V.188, H2O.24, H2O.27
- 3 x 6EZ: (3-exo)-N-(4-amino-4'-fluoro[1,1'-biphenyl]-3-yl)-8-oxabicyclo[3.2.1]octane-3-carboxamide(Non-covalent)
6EZ.4: 20 residues within 4Å:- Chain A: Y.19, M.25, R.29, F.104, G.133, L.134, H.135, H.136, G.144, F.145, C.146, D.171, H.173, F.200, D.259, L.266, G.295, G.296, Y.298
- Ligands: ZN.1
11 PLIP interactions:11 interactions with chain A- Hydrophobic interactions: A:L.134, A:L.134, A:L.134, A:F.145, A:F.145, A:F.145, A:F.200, A:L.266
- Hydrogen bonds: A:H.136, A:G.144, A:Y.298
6EZ.14: 20 residues within 4Å:- Chain B: Y.19, M.25, R.29, F.104, G.133, L.134, H.135, H.136, G.144, F.145, C.146, D.171, H.173, F.200, D.259, L.266, G.295, G.296, Y.298
- Ligands: ZN.11
10 PLIP interactions:10 interactions with chain B- Hydrophobic interactions: B:L.134, B:L.134, B:L.134, B:F.145, B:F.145, B:F.200, B:L.266
- Hydrogen bonds: B:H.136, B:G.144, B:Y.298
6EZ.28: 20 residues within 4Å:- Chain C: Y.19, M.25, R.29, F.104, G.133, L.134, H.135, H.136, G.144, F.145, C.146, D.171, H.173, F.200, D.259, L.266, G.295, G.296, Y.298
- Ligands: ZN.25
9 PLIP interactions:9 interactions with chain C- Hydrophobic interactions: C:L.134, C:L.134, C:L.134, C:F.145, C:F.145, C:F.200, C:L.266
- Hydrogen bonds: C:H.136, C:G.144
- 5 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
PEG.5: 4 residues within 4Å:- Chain A: G.15, Y.18, H.28, Y.331
2 PLIP interactions:2 interactions with chain A- Water bridges: A:H.28, A:Y.331
PEG.6: 5 residues within 4Å:- Chain A: L.159, K.160, Y.161, Q.163, R.187
2 PLIP interactions:2 interactions with chain A- Water bridges: A:Q.163, A:R.187
PEG.16: 3 residues within 4Å:- Chain B: Y.18, H.28, Y.331
1 PLIP interactions:1 interactions with chain B- Water bridges: B:Y.331
PEG.17: 3 residues within 4Å:- Chain B: K.84, Q.85, R.88
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:R.88
PEG.30: 4 residues within 4Å:- Chain C: Q.122, Q.123, T.124, D.125
No protein-ligand interaction detected (PLIP)- 2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)
PG4.7: 4 residues within 4Å:- Chain A: R.301, E.330, Y.331, G.333
4 PLIP interactions:4 interactions with chain A- Water bridges: A:R.265, A:R.265, A:R.265, A:R.265
PG4.31: 8 residues within 4Å:- Chain B: N.344, T.346
- Chain C: L.159, K.160, Y.161, H.162, Q.163, R.187
4 PLIP interactions:2 interactions with chain C, 2 interactions with chain B- Water bridges: C:L.159, C:R.187
- Hydrogen bonds: B:N.344, B:T.346
- 3 x PG5: 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE(Non-covalent)
PG5.8: 4 residues within 4Å:- Chain A: D.13, N.16, Y.17, D.99
No protein-ligand interaction detected (PLIP)PG5.18: 6 residues within 4Å:- Chain B: R.301, E.330, Y.331, G.333, P.334
- Ligands: PGE.32
No protein-ligand interaction detected (PLIP)PG5.19: 6 residues within 4Å:- Chain B: K.274, N.321, H.339
- Chain C: E.57, T.60, K.61
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:K.274
- Water bridges: B:Y.309
- 9 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)
PGE.9: 4 residues within 4Å:- Chain A: K.61, Y.62, A.181, R.187
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:R.187
- Water bridges: A:K.61, A:R.187
PGE.10: 8 residues within 4Å:- Chain A: Q.163, R.164, D.186, Y.217, M.246, Y.247, Q.248, P.369
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:Q.163
PGE.20: 5 residues within 4Å:- Chain B: D.13, N.16, Y.17, D.99, E.103
2 PLIP interactions:2 interactions with chain B- Water bridges: B:D.99, B:D.99
PGE.21: 7 residues within 4Å:- Chain B: D.11, D.13, Y.17, R.50, K.53, E.103, L.107
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:D.13, B:R.50, B:E.103
PGE.22: 7 residues within 4Å:- Chain B: R.164, D.186, Y.217, M.246, Y.247, Q.248, P.369
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:R.164
PGE.23: 5 residues within 4Å:- Chain B: S.262, G.263, R.265, R.301, N.302
6 PLIP interactions:6 interactions with chain B- Hydrogen bonds: B:R.265, B:R.265, B:R.301, B:R.301, B:N.302
- Water bridges: B:N.302
PGE.24: 7 residues within 4Å:- Chain B: K.4, D.125, M.126, K.284, N.287, L.288, P.289
2 PLIP interactions:2 interactions with chain B- Water bridges: B:T.124, B:K.284
PGE.32: 8 residues within 4Å:- Chain B: P.334
- Chain C: Y.62, L.156, A.181, F.182, T.185, R.187
- Ligands: PG5.18
3 PLIP interactions:2 interactions with chain C, 1 interactions with chain B- Hydrogen bonds: C:R.187
- Water bridges: C:R.187, B:D.335
PGE.33: 4 residues within 4Å:- Chain C: D.13, N.16, Y.17, D.99
No protein-ligand interaction detected (PLIP)- 2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Wagner, F.F. et al., Kinetic and structural insights into the binding of histone deacetylase 1 and 2 (HDAC1, 2) inhibitors. Bioorg.Med.Chem. (2016)
- Release Date
- 2016-08-31
- Peptides
- Histone deacetylase 2: ABC
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
C
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.72 Å
- Oligo State
- homo-trimer
- Ligands
- 3 x ZN: ZINC ION(Non-covalent)
- 6 x CA: CALCIUM ION(Non-covalent)
- 3 x 6EZ: (3-exo)-N-(4-amino-4'-fluoro[1,1'-biphenyl]-3-yl)-8-oxabicyclo[3.2.1]octane-3-carboxamide(Non-covalent)
- 5 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
- 2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)
- 3 x PG5: 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE(Non-covalent)
- 9 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)
- 2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Wagner, F.F. et al., Kinetic and structural insights into the binding of histone deacetylase 1 and 2 (HDAC1, 2) inhibitors. Bioorg.Med.Chem. (2016)
- Release Date
- 2016-08-31
- Peptides
- Histone deacetylase 2: ABC
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
C