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Zinc in PDB 5kh7: Crystal Structure of Fragment (3-[6-Oxo-3-(3-Pyridinyl)-1(6H)- Pyridazinyl]Propanoic Acid) Bound in the Ubiquitin Binding Pocket of the HDAC6 Zinc-Finger Domain

Enzymatic activity of Crystal Structure of Fragment (3-[6-Oxo-3-(3-Pyridinyl)-1(6H)- Pyridazinyl]Propanoic Acid) Bound in the Ubiquitin Binding Pocket of the HDAC6 Zinc-Finger Domain

All present enzymatic activity of Crystal Structure of Fragment (3-[6-Oxo-3-(3-Pyridinyl)-1(6H)- Pyridazinyl]Propanoic Acid) Bound in the Ubiquitin Binding Pocket of the HDAC6 Zinc-Finger Domain:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of Fragment (3-[6-Oxo-3-(3-Pyridinyl)-1(6H)- Pyridazinyl]Propanoic Acid) Bound in the Ubiquitin Binding Pocket of the HDAC6 Zinc-Finger Domain, PDB code: 5kh7 was solved by R.J.Harding, J.Walker, M.Ravichandran, R.Ferreira De Freitas, M.Schapira, C.Bountra, A.M.Edwards, V.Santhakumar, C.M.Arrowsmith, Structuralgenomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.47 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 40.719, 43.776, 55.924, 90.00, 90.00, 90.00
R / Rfree (%) 14.6 / 18.3

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Fragment (3-[6-Oxo-3-(3-Pyridinyl)-1(6H)- Pyridazinyl]Propanoic Acid) Bound in the Ubiquitin Binding Pocket of the HDAC6 Zinc-Finger Domain (pdb code 5kh7). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of Fragment (3-[6-Oxo-3-(3-Pyridinyl)-1(6H)- Pyridazinyl]Propanoic Acid) Bound in the Ubiquitin Binding Pocket of the HDAC6 Zinc-Finger Domain, PDB code: 5kh7:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 5kh7

Go back to Zinc Binding Sites List in 5kh7
Zinc binding site 1 out of 3 in the Crystal Structure of Fragment (3-[6-Oxo-3-(3-Pyridinyl)-1(6H)- Pyridazinyl]Propanoic Acid) Bound in the Ubiquitin Binding Pocket of the HDAC6 Zinc-Finger Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Fragment (3-[6-Oxo-3-(3-Pyridinyl)-1(6H)- Pyridazinyl]Propanoic Acid) Bound in the Ubiquitin Binding Pocket of the HDAC6 Zinc-Finger Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1301

b:6.1
occ:1.00
 NE2 A:HIS1164 2.1 6.0 1.0
ND1 A:HIS1170 2.1 5.7 1.0
SG A:CYS1145 2.3 5.2 1.0
SG A:CYS1148 2.4 7.4 1.0
CE1 A:HIS1164 3.0 6.1 1.0
CE1 A:HIS1170 3.1 5.8 1.0
CG A:HIS1170 3.1 5.7 1.0
CB A:CYS1145 3.1 4.8 1.0
CD2 A:HIS1164 3.1 5.9 1.0
CB A:HIS1170 3.5 5.5 1.0
CB A:CYS1148 3.5 6.2 1.0
N A:CYS1148 3.8 5.5 1.0
ND1 A:HIS1164 4.1 6.1 1.0
CA A:CYS1148 4.2 5.8 1.0
NE2 A:HIS1170 4.2 5.9 1.0
CG A:HIS1164 4.2 6.0 1.0
CD2 A:HIS1170 4.2 5.8 1.0
OG A:SER1168 4.3 7.3 1.0
CB A:SER1147 4.5 5.1 1.0
CA A:CYS1145 4.6 4.5 1.0
C A:SER1147 4.7 5.8 1.0
O A:HOH1475 4.8 26.9 1.0
CB A:SER1168 4.8 7.4 1.0
C A:CYS1148 4.8 5.5 1.0
N A:TYR1149 4.9 5.1 1.0
N A:SER1147 4.9 5.0 1.0
CA A:SER1147 4.9 5.2 1.0
CA A:HIS1170 5.0 5.6 1.0

Zinc binding site 2 out of 3 in 5kh7

Go back to Zinc Binding Sites List in 5kh7
Zinc binding site 2 out of 3 in the Crystal Structure of Fragment (3-[6-Oxo-3-(3-Pyridinyl)-1(6H)- Pyridazinyl]Propanoic Acid) Bound in the Ubiquitin Binding Pocket of the HDAC6 Zinc-Finger Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Fragment (3-[6-Oxo-3-(3-Pyridinyl)-1(6H)- Pyridazinyl]Propanoic Acid) Bound in the Ubiquitin Binding Pocket of the HDAC6 Zinc-Finger Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1302

b:6.2
occ:1.00
 ND1 A:HIS1160 2.1 6.7 1.0
SG A:CYS1136 2.3 6.8 1.0
SG A:CYS1153 2.3 5.9 1.0
SG A:CYS1133 2.4 6.0 1.0
CE1 A:HIS1160 3.0 6.7 1.0
CG A:HIS1160 3.1 6.2 1.0
CB A:CYS1133 3.3 6.2 1.0
CB A:CYS1153 3.3 5.2 1.0
CB A:CYS1136 3.4 7.7 1.0
CB A:HIS1160 3.5 6.0 1.0
N A:CYS1136 3.7 7.8 1.0
N A:CYS1153 4.0 4.8 1.0
CB A:ASN1158 4.0 8.3 1.0
CA A:CYS1136 4.1 7.6 1.0
NE2 A:HIS1160 4.2 6.8 1.0
CG2 A:THR1138 4.2 8.7 1.0
CD2 A:HIS1160 4.2 6.8 1.0
CA A:CYS1153 4.3 4.9 1.0
ND2 A:ASN1158 4.4 8.8 1.0
CB A:ASP1135 4.5 7.3 0.3
CB A:ASP1135 4.5 10.9 0.7
N A:HIS1160 4.6 5.9 1.0
CA A:HIS1160 4.6 5.8 1.0
CA A:CYS1133 4.7 6.2 1.0
C A:ASP1135 4.7 7.7 0.3
CG A:ASN1158 4.8 9.0 1.0
C A:ASP1135 4.8 8.8 0.7
C A:CYS1136 4.8 7.6 1.0
CA A:ASN1158 4.9 7.7 1.0
N A:GLY1137 5.0 7.5 1.0
N A:ASN1158 5.0 7.6 1.0
CA A:ASP1135 5.0 7.6 0.3
N A:ASP1135 5.0 7.9 0.3

Zinc binding site 3 out of 3 in 5kh7

Go back to Zinc Binding Sites List in 5kh7
Zinc binding site 3 out of 3 in the Crystal Structure of Fragment (3-[6-Oxo-3-(3-Pyridinyl)-1(6H)- Pyridazinyl]Propanoic Acid) Bound in the Ubiquitin Binding Pocket of the HDAC6 Zinc-Finger Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Fragment (3-[6-Oxo-3-(3-Pyridinyl)-1(6H)- Pyridazinyl]Propanoic Acid) Bound in the Ubiquitin Binding Pocket of the HDAC6 Zinc-Finger Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1303

b:6.1
occ:1.00
 ND1 A:HIS1115 2.2 6.2 1.0
SG A:CYS1183 2.3 4.8 1.0
SG A:CYS1113 2.3 6.5 1.0
SG A:CYS1186 2.3 6.2 1.0
CE1 A:HIS1115 3.1 6.1 1.0
CG A:HIS1115 3.2 6.2 1.0
CB A:CYS1113 3.3 6.6 1.0
CB A:CYS1183 3.3 4.8 1.0
CB A:CYS1186 3.3 6.6 1.0
CB A:HIS1115 3.5 6.2 1.0
N A:CYS1186 3.9 6.8 1.0
N A:HIS1115 3.9 6.3 1.0
CD A:PRO1114 4.1 7.1 1.0
NE2 A:HIS1115 4.2 6.3 1.0
CA A:CYS1186 4.2 6.7 1.0
CD2 A:HIS1115 4.3 6.3 1.0
N A:PRO1114 4.3 6.9 1.0
CA A:HIS1115 4.3 6.5 1.0
CA A:CYS1113 4.5 6.7 1.0
C A:CYS1113 4.5 6.6 1.0
CB A:TYR1185 4.6 6.3 1.0
CG A:PRO1114 4.6 7.3 1.0
CA A:CYS1183 4.7 4.8 1.0
O A:HOH1501 4.8 11.9 1.0
C A:TYR1185 4.9 6.5 1.0
C A:PRO1114 4.9 7.0 1.0

Reference:

R.J.Harding, R.Ferreira De Freitas, P.Collins, I.Franzoni, M.Ravichandran, H.Ouyang, K.A.Juarez-Ornelas, M.Lautens, M.Schapira, F.Von Delft, V.Santhakumar, C.H.Arrowsmith. Small Molecule Antagonists of the Interaction Between the Histone Deacetylase 6 Zinc-Finger Domain and Ubiquitin. J. Med. Chem. V. 60 9090 2017.
ISSN: ISSN 1520-4804
PubMed: 29019676
DOI: 10.1021/ACS.JMEDCHEM.7B00933
Page generated: Sun Oct 27 20:23:54 2024

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