SMTL ID : 6gjk.1

A degradation product of PD 404182 (P2742) bound to Histone Deacetylase-like Amidohydrolase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.47 Å

Oligo State

homo-tetramer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: D.186, H.188, D.274 Ligands: ACT.9 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.186, A:D.186, A:H.188, A:D.274, ACT.9 ZN.11: 4 residues within 4Å: Chain B: D.186, H.188, D.274 Ligands: ACT.21 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.186, B:D.186, B:H.188, B:D.274 ZN.22: 4 residues within 4Å: Chain C: D.186, H.188, D.274 Ligands: ACT.30 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Ligand interactions Metal complexes: C:D.186, C:D.186, C:H.188, C:D.274, ACT.30 ZN.32: 4 residues within 4Å: Chain D: D.186, H.188, D.274 Ligands: ACT.42 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Ligand interactions Metal complexes: D:D.186, D:D.186, D:H.188, D:D.274, ACT.42

8 x K: POTASSIUM ION(Non-covalent)

K.2: 7 residues within 4Å: Chain A: D.184, D.186, H.188, G.190, S.207, L.208, H.209 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.186, A:H.188, A:S.207 K.3: 5 residues within 4Å: Chain A: W.197, D.200, V.203, T.205, Y.232 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:W.197, A:D.200, A:V.203, A:Y.232, H2O.5 K.12: 7 residues within 4Å: Chain B: D.184, D.186, H.188, G.190, S.207, L.208, H.209 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.186, B:H.188, B:S.207, B:L.208 K.13: 5 residues within 4Å: Chain B: W.197, D.200, V.203, T.205, Y.232 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.200, B:V.203, B:Y.232, H2O.22, H2O.23 K.23: 7 residues within 4Å: Chain C: D.184, D.186, H.188, G.190, S.207, L.208, H.209 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.186, C:H.188, C:S.207 K.24: 5 residues within 4Å: Chain C: W.197, D.200, V.203, T.205, Y.232 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:W.197, C:D.200, C:V.203, C:Y.232, H2O.37 K.33: 7 residues within 4Å: Chain D: D.184, D.186, H.188, G.190, S.207, L.208, H.209 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.186, D:H.188, D:S.207, D:L.208 K.34: 5 residues within 4Å: Chain D: W.197, D.200, V.203, T.205, Y.232 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.200, D:V.203, D:Y.232, H2O.54, H2O.55

4 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.4: 5 residues within 4Å: Chain A: E.178, R.179, P.201, Y.232, R.263 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.179, A:R.263 1PE.14: 5 residues within 4Å: Chain B: E.178, R.179, P.201, N.228, Y.232 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.179, B:N.228 Water bridges: B:R.179, B:R.263 1PE.25: 5 residues within 4Å: Chain C: E.178, R.179, P.201, Y.232, R.263 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.179, C:R.263 1PE.35: 5 residues within 4Å: Chain D: E.178, R.179, P.201, N.228, Y.232 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:R.179, D:N.228 Water bridges: D:R.179, D:R.263

12 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.5: 2 residues within 4Å: Chain A: D.358, R.361 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.361 PEG.6: 4 residues within 4Å: Chain A: N.191, Q.194, D.195, W.198 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.191, A:Q.194, A:D.195, A:D.195, A:D.195 Water bridges: A:N.191 PEG.15: 1 residues within 4Å: Chain B: R.361 No protein-ligand interaction detected (PLIP) PEG.16: 6 residues within 4Å: Chain B: Y.11, W.13, P.67, I.68 Ligands: F0Z.7, MLT.10 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:W.13 PEG.17: 4 residues within 4Å: Chain B: Q.194, W.198, D.217, E.223 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.217 PEG.18: 5 residues within 4Å: Chain B: R.80, A.81, H.152, D.195, I.196 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.195 PEG.26: 2 residues within 4Å: Chain C: D.358, R.361 1 PLIP interactions: 1 interactions with chain C Water bridges: C:R.361 PEG.27: 4 residues within 4Å: Chain C: N.191, Q.194, D.195, W.198 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:N.191, C:Q.194, C:D.195, C:D.195, C:D.195 Water bridges: C:N.191 PEG.36: 1 residues within 4Å: Chain D: R.361 No protein-ligand interaction detected (PLIP) PEG.37: 6 residues within 4Å: Chain D: Y.11, W.13, P.67, I.68 Ligands: F0Z.28, MLT.31 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:W.13 PEG.38: 4 residues within 4Å: Chain D: Q.194, W.198, D.217, E.223 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.217 PEG.39: 5 residues within 4Å: Chain D: R.80, A.81, H.152, D.195, I.196 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.195

8 x F0Z: 2-(1,4,5,6-tetrahydropyrimidin-2-yl)benzenethiol(Non-covalent)

F0Z.7: 8 residues within 4Å: Chain A: C.57, I.62, E.63, P.67 Chain B: W.13, T.15 Ligands: MLT.10, PEG.16 No protein-ligand interaction detected (PLIP) F0Z.8: 5 residues within 4Å: Chain A: L.256, R.260, C.301, D.304, I.305 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:R.260, A:R.260, A:D.304, A:I.305 Hydrogen bonds: A:D.304, A:D.304 pi-Cation interactions: A:R.260 F0Z.19: 7 residues within 4Å: Chain A: W.13, T.15 Chain B: C.57, I.62, E.63, P.67 Ligands: MLT.10 1 PLIP interactions: 1 interactions with chain B Water bridges: B:E.63 F0Z.20: 6 residues within 4Å: Chain B: L.256, P.257, R.260, D.300, C.301, D.304 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.256 Hydrogen bonds: B:D.304 F0Z.28: 8 residues within 4Å: Chain C: C.57, I.62, E.63, P.67 Chain D: W.13, T.15 Ligands: MLT.31, PEG.37 No protein-ligand interaction detected (PLIP) F0Z.29: 5 residues within 4Å: Chain C: L.256, R.260, C.301, D.304, I.305 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:R.260, C:R.260, C:D.304, C:I.305 Hydrogen bonds: C:D.304, C:D.304 pi-Cation interactions: C:R.260 F0Z.40: 7 residues within 4Å: Chain C: W.13, T.15 Chain D: C.57, I.62, E.63, P.67 Ligands: MLT.31 1 PLIP interactions: 1 interactions with chain D Water bridges: D:E.63 F0Z.41: 6 residues within 4Å: Chain D: L.256, P.257, R.260, D.300, C.301, D.304 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:L.256 Hydrogen bonds: D:D.304

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.9: 9 residues within 4Å: Chain A: H.148, H.149, G.157, D.186, H.188, D.274, G.316, Y.318 Ligands: ZN.1 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:H.148, A:H.149, A:H.188 ACT.21: 10 residues within 4Å: Chain B: H.148, H.149, G.157, F.158, D.186, H.188, D.274, G.316, Y.318 Ligands: ZN.11 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.158 Hydrogen bonds: B:Y.318, B:Y.318 Salt bridges: B:H.148, B:H.149, B:H.188 ACT.30: 9 residues within 4Å: Chain C: H.148, H.149, G.157, D.186, H.188, D.274, G.316, Y.318 Ligands: ZN.22 3 PLIP interactions: 3 interactions with chain C Salt bridges: C:H.148, C:H.149, C:H.188 ACT.42: 10 residues within 4Å: Chain D: H.148, H.149, G.157, F.158, D.186, H.188, D.274, G.316, Y.318 Ligands: ZN.32 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:F.158 Hydrogen bonds: D:Y.318 Salt bridges: D:H.148, D:H.149, D:H.188

2 x MLT: D-MALATE(Non-covalent)

MLT.10: 6 residues within 4Å: Chain A: H.53, C.57 Chain B: H.53 Ligands: F0Z.7, PEG.16, F0Z.19 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Water bridges: B:E.54 Salt bridges: B:H.53, A:H.53 Hydrogen bonds: A:H.53 MLT.31: 6 residues within 4Å: Chain C: H.53, C.57 Chain D: H.53 Ligands: F0Z.28, PEG.37, F0Z.40 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Water bridges: D:E.54 Salt bridges: D:H.53, C:H.53 Hydrogen bonds: C:H.53

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Muth, M. et al., Covalent inhibition of histone deacetylase 8 by 3,4-dihydro-2H-pyrimido[1,2-c][1,3]benzothiazin-6-imine. Biochim Biophys Acta Gen Subj (2019)

Release Date

2019-01-16

Peptides

Histone deacetylase-like amidohydrolase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Histone deacetylase-like amidohydrolase

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