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Zinc in PDB 5wpb: Crystal Structure of Fragment 3-(3-(Pyridin-2-Ylmethoxy)Quinoxalin-2- Yl)Propanoic Acid Bound in the Ubiquitin Binding Pocket of the HDAC6 Zinc-Finger Domain

Enzymatic activity of Crystal Structure of Fragment 3-(3-(Pyridin-2-Ylmethoxy)Quinoxalin-2- Yl)Propanoic Acid Bound in the Ubiquitin Binding Pocket of the HDAC6 Zinc-Finger Domain

All present enzymatic activity of Crystal Structure of Fragment 3-(3-(Pyridin-2-Ylmethoxy)Quinoxalin-2- Yl)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-(3-(Pyridin-2-Ylmethoxy)Quinoxalin-2- Yl)Propanoic Acid Bound in the Ubiquitin Binding Pocket of the HDAC6 Zinc-Finger Domain, PDB code: 5wpb was solved by R.J.Harding, W.Tempel, R.Ferreira De Freitas, I.Franzoni, M.Ravichandran, M.Lautens, V.Santhakumar, M.Schapira, C.Bountra, A.M.Edwards, C.H.Arrowsmith, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.85 / 1.55
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 40.850, 43.740, 55.760, 90.00, 90.00, 90.00
R / Rfree (%) 14.3 / 16.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Fragment 3-(3-(Pyridin-2-Ylmethoxy)Quinoxalin-2- Yl)Propanoic Acid Bound in the Ubiquitin Binding Pocket of the HDAC6 Zinc-Finger Domain (pdb code 5wpb). 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-(3-(Pyridin-2-Ylmethoxy)Quinoxalin-2- Yl)Propanoic Acid Bound in the Ubiquitin Binding Pocket of the HDAC6 Zinc-Finger Domain, PDB code: 5wpb:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 5wpb

Go back to Zinc Binding Sites List in 5wpb
Zinc binding site 1 out of 3 in the Crystal Structure of Fragment 3-(3-(Pyridin-2-Ylmethoxy)Quinoxalin-2- Yl)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-(3-(Pyridin-2-Ylmethoxy)Quinoxalin-2- Yl)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:7.6
occ:1.00
 ND1 A:HIS1170 2.1 6.6 1.0
NE2 A:HIS1164 2.1 7.0 1.0
SG A:CYS1148 2.3 7.0 1.0
SG A:CYS1145 2.3 5.6 1.0
CE1 A:HIS1164 3.0 7.2 1.0
CE1 A:HIS1170 3.0 6.9 1.0
CG A:HIS1170 3.1 6.4 1.0
CD2 A:HIS1164 3.1 6.9 1.0
CB A:CYS1145 3.2 5.5 1.0
CB A:CYS1148 3.4 7.0 1.0
CB A:HIS1170 3.5 6.5 1.0
N A:CYS1148 3.7 6.7 1.0
CA A:CYS1148 4.0 6.6 1.0
NE2 A:HIS1170 4.1 7.3 1.0
ND1 A:HIS1164 4.1 7.6 1.0
CD2 A:HIS1170 4.2 7.0 1.0
CG A:HIS1164 4.2 6.8 1.0
OG A:SER1168 4.3 7.8 1.0
CB A:SER1147 4.5 6.1 1.0
CA A:CYS1145 4.6 5.4 1.0
C A:CYS1148 4.7 6.7 1.0
C A:SER1147 4.7 6.6 1.0
CB A:SER1168 4.8 8.0 1.0
N A:TYR1149 4.8 6.4 1.0
CA A:SER1147 4.9 6.2 1.0
N A:SER1147 5.0 6.0 1.0

Zinc binding site 2 out of 3 in 5wpb

Go back to Zinc Binding Sites List in 5wpb
Zinc binding site 2 out of 3 in the Crystal Structure of Fragment 3-(3-(Pyridin-2-Ylmethoxy)Quinoxalin-2- Yl)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-(3-(Pyridin-2-Ylmethoxy)Quinoxalin-2- Yl)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:8.5
occ:1.00
 ND1 A:HIS1160 2.1 8.2 1.0
SG A:CYS1136 2.3 7.8 1.0
SG A:CYS1153 2.3 6.9 1.0
SG A:CYS1133 2.4 6.7 1.0
CE1 A:HIS1160 3.0 8.4 1.0
CG A:HIS1160 3.1 8.2 1.0
CB A:CYS1133 3.3 6.9 1.0
CB A:CYS1153 3.3 6.9 1.0
CB A:CYS1136 3.5 8.7 1.0
CB A:HIS1160 3.5 7.6 1.0
N A:CYS1136 3.7 9.1 1.0
N A:CYS1153 4.0 6.1 1.0
CB A:ASN1158 4.0 10.1 1.0
CG2 A:THR1138 4.1 8.9 1.0
CA A:CYS1136 4.1 9.2 1.0
NE2 A:HIS1160 4.2 9.0 1.0
CD2 A:HIS1160 4.2 9.0 1.0
CA A:CYS1153 4.3 6.5 1.0
ND2 A:ASN1158 4.5 10.6 1.0
N A:HIS1160 4.6 7.7 1.0
CB A:ASP1135 4.6 13.0 1.0
CA A:HIS1160 4.6 7.5 1.0
CA A:CYS1133 4.7 7.0 1.0
C A:ASP1135 4.8 11.5 1.0
CG A:ASN1158 4.8 10.7 1.0
C A:CYS1136 4.8 9.0 1.0
CA A:ASN1158 4.9 9.6 1.0
N A:GLY1137 4.9 8.7 1.0

Zinc binding site 3 out of 3 in 5wpb

Go back to Zinc Binding Sites List in 5wpb
Zinc binding site 3 out of 3 in the Crystal Structure of Fragment 3-(3-(Pyridin-2-Ylmethoxy)Quinoxalin-2- Yl)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-(3-(Pyridin-2-Ylmethoxy)Quinoxalin-2- Yl)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:7.3
occ:1.00
 ND1 A:HIS1115 2.1 6.5 1.0
SG A:CYS1183 2.3 5.5 1.0
SG A:CYS1113 2.3 5.9 1.0
SG A:CYS1186 2.3 7.0 1.0
CE1 A:HIS1115 3.1 6.4 1.0
CG A:HIS1115 3.1 6.3 1.0
CB A:CYS1113 3.2 6.2 1.0
CB A:CYS1183 3.3 6.1 1.0
CB A:CYS1186 3.3 7.2 1.0
CB A:HIS1115 3.5 6.4 1.0
N A:CYS1186 3.9 7.3 1.0
N A:HIS1115 4.0 6.7 1.0
CD A:PRO1114 4.1 7.3 1.0
NE2 A:HIS1115 4.2 6.5 1.0
CA A:CYS1186 4.2 7.8 1.0
CD2 A:HIS1115 4.3 6.6 1.0
N A:PRO1114 4.3 7.2 1.0
CA A:HIS1115 4.4 6.6 1.0
CA A:CYS1113 4.5 6.6 1.0
CB A:TYR1185 4.5 7.3 1.0
C A:CYS1113 4.6 6.5 1.0
CA A:CYS1183 4.7 6.0 1.0
CG A:PRO1114 4.7 7.8 1.0
O A:HOH1484 4.9 12.2 1.0
C A:TYR1185 4.9 7.2 1.0
C A:PRO1114 4.9 7.2 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: Mon Oct 28 14:36:55 2024

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