SMTL ID : 5g1c.1

Structure of HDAC like protein from Bordetella Alcaligenes bound the photoswitchable pyrazole Inhibitor CEW395

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.81 Å

Oligo State

homo-tetramer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: D.181, H.183, D.269 Ligands: 9RB.4 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.181, A:D.181, A:H.183, A:D.269, 9RB.4 ZN.10: 5 residues within 4Å: Chain B: H.143, D.181, H.183, D.269 Ligands: 9RB.13 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:D.181, B:D.181, B:H.183, B:D.269, 9RB.13 ZN.18: 4 residues within 4Å: Chain C: D.181, H.183, D.269 Ligands: 9RB.21 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Ligand interactions Metal complexes: C:D.181, C:D.181, C:H.183, C:D.269, 9RB.21 ZN.27: 5 residues within 4Å: Chain D: H.143, D.181, H.183, D.269 Ligands: 9RB.30 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Ligand interactions Metal complexes: D:D.181, D:D.181, D:H.183, D:D.269, 9RB.30

8 x K: POTASSIUM ION(Non-covalent)

K.2: 5 residues within 4Å: Chain A: D.179, D.181, H.183, S.202, L.203 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.179, A:D.181, A:H.183, A:S.202, A:L.203 K.3: 5 residues within 4Å: Chain A: W.192, D.195, V.198, T.200, Y.227 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.195, A:V.198, A:Y.227, H2O.12, H2O.12 K.11: 5 residues within 4Å: Chain B: D.179, D.181, H.183, S.202, L.203 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.179, B:D.181, B:H.183, B:S.202, B:L.203 K.12: 5 residues within 4Å: Chain B: W.192, D.195, V.198, T.200, Y.227 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.195, B:V.198, B:Y.227, H2O.31, H2O.32 K.19: 5 residues within 4Å: Chain C: D.179, D.181, H.183, S.202, L.203 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.179, C:D.181, C:H.183, C:S.202, C:L.203 K.20: 5 residues within 4Å: Chain C: W.192, D.195, V.198, T.200, Y.227 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.195, C:V.198, C:Y.227, H2O.50, H2O.50 K.28: 5 residues within 4Å: Chain D: D.179, D.181, H.183, S.202, L.203 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.179, D:D.181, D:H.183, D:S.202, D:L.203 K.29: 5 residues within 4Å: Chain D: W.192, D.195, V.198, T.200, Y.227 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.195, D:V.198, D:Y.227, H2O.69, H2O.70

4 x 9RB: (2E)-N-hydroxy-3-{4-[(E)-(1,3,5-trimethyl-1H-pyrazol-4-yl)diazenyl]phenyl}prop-2-enamide(Non-covalent)

9RB.4: 12 residues within 4Å: Chain A: L.22, H.143, H.144, G.152, F.153, D.181, H.183, F.209, D.269, Y.313 Chain C: F.342 Ligands: ZN.1 11 PLIP interactions: 2 interactions with chain C, 9 interactions with chain A Hydrophobic interactions: C:F.342, C:F.342, A:L.22, A:L.22, A:F.153, A:F.209, A:F.209, A:F.209 Hydrogen bonds: A:H.144, A:Y.313 pi-Stacking: A:F.153 9RB.13: 14 residues within 4Å: Chain B: L.22, A.23, I.101, H.143, H.144, G.152, F.153, D.181, H.183, F.209, D.269, Y.313 Chain D: F.342 Ligands: ZN.10 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: B:L.22, B:L.22, B:A.23, B:F.153, B:F.153, B:F.209, B:F.209, D:F.342, D:F.342 Hydrogen bonds: B:H.144 9RB.21: 12 residues within 4Å: Chain A: F.342 Chain C: L.22, H.143, H.144, G.152, F.153, D.181, H.183, F.209, D.269, Y.313 Ligands: ZN.18 11 PLIP interactions: 9 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:L.22, C:L.22, C:F.153, C:F.209, C:F.209, C:F.209, A:F.342, A:F.342 Hydrogen bonds: C:H.144, C:Y.313 pi-Stacking: C:F.153 9RB.30: 14 residues within 4Å: Chain B: F.342 Chain D: L.22, A.23, I.101, H.143, H.144, G.152, F.153, D.181, H.183, F.209, D.269, Y.313 Ligands: ZN.27 10 PLIP interactions: 8 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: D:L.22, D:L.22, D:A.23, D:F.153, D:F.153, D:F.209, D:F.209, B:F.342, B:F.342 Hydrogen bonds: D:H.144

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

1PE.5: 6 residues within 4Å: Chain A: E.173, R.174, P.196, N.223, Y.227, R.370 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.174, A:R.370 1PE.14: 6 residues within 4Å: Chain B: E.173, R.174, P.196, N.223, Y.227, R.258 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.174 Water bridges: B:N.223 1PE.22: 6 residues within 4Å: Chain C: E.173, R.174, P.196, N.223, Y.227, R.370 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.174, C:R.370 1PE.31: 6 residues within 4Å: Chain D: E.173, R.174, P.196, N.223, Y.227, R.258 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.174 Water bridges: D:N.223

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

PEG.6: 2 residues within 4Å: Chain A: T.350 Ligands: PEG.24 No protein-ligand interaction detected (PLIP) PEG.7: 8 residues within 4Å: Chain A: H.206, P.232, L.233, P.234, P.235, A.358, E.361 Ligands: PEG.23 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.361 PEG.8: 2 residues within 4Å: Chain A: R.356 Ligands: PEG.9 No protein-ligand interaction detected (PLIP) PEG.9: 4 residues within 4Å: Chain A: D.353, A.354, A.357 Ligands: PEG.8 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.357 PEG.15: 6 residues within 4Å: Chain B: K.86, S.89, N.90, G.107, L.109, E.110 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.110 PEG.16: 2 residues within 4Å: Chain B: D.284, H.340 2 PLIP interactions: 2 interactions with chain B Water bridges: B:D.284, B:Q.288 PEG.17: 5 residues within 4Å: Chain B: N.239, A.240, L.243, D.284, Q.288 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.239, B:D.284, B:D.284, B:Q.288 PEG.23: 2 residues within 4Å: Chain C: T.350 Ligands: PEG.7 No protein-ligand interaction detected (PLIP) PEG.24: 8 residues within 4Å: Chain C: H.206, P.232, L.233, P.234, P.235, A.358, E.361 Ligands: PEG.6 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.361 PEG.25: 2 residues within 4Å: Chain C: R.356 Ligands: PEG.26 No protein-ligand interaction detected (PLIP) PEG.26: 4 residues within 4Å: Chain C: D.353, A.354, A.357 Ligands: PEG.25 1 PLIP interactions: 1 interactions with chain C Water bridges: C:A.357 PEG.32: 6 residues within 4Å: Chain D: K.86, S.89, N.90, G.107, L.109, E.110 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.110 PEG.33: 2 residues within 4Å: Chain D: D.284, H.340 2 PLIP interactions: 2 interactions with chain D Water bridges: D:D.284, D:Q.288 PEG.34: 5 residues within 4Å: Chain D: N.239, A.240, L.243, D.284, Q.288 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:N.239, D:D.284, D:D.284, D:Q.288

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Weston, C.E. et al., Toward Photopharmacological Antimicrobial Chemotherapy Using Photoswitchable Amidohydrolase Inhibitors. ACS Infect Dis (2017)

Release Date

2016-11-23

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