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Zinc in PDB 6cee: Crystal Structure of Fragment 3-(1-Methyl-2-Oxo-1,2-Dihydroquinoxalin- 3-Yl)Propionic Acid Bound in the Ubiquitin Binding Pocket of the HDAC6 Zinc-Finger Domain

Enzymatic activity of Crystal Structure of Fragment 3-(1-Methyl-2-Oxo-1,2-Dihydroquinoxalin- 3-Yl)Propionic Acid Bound in the Ubiquitin Binding Pocket of the HDAC6 Zinc-Finger Domain

All present enzymatic activity of Crystal Structure of Fragment 3-(1-Methyl-2-Oxo-1,2-Dihydroquinoxalin- 3-Yl)Propionic 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-(1-Methyl-2-Oxo-1,2-Dihydroquinoxalin- 3-Yl)Propionic Acid Bound in the Ubiquitin Binding Pocket of the HDAC6 Zinc-Finger Domain, PDB code: 6cee was solved by R.J.Harding, L.Halabelian, R.Ferreira De Freitas, I.Franzoni, M.Ravichandran, M.Lautens, V.Santhakumar, M.Schapira, C.Bountra, A.M.Edwards, C.M.Arrowsmith, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.55
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 40.720, 44.110, 55.910, 90.00, 90.00, 90.00
R / Rfree (%) 15.3 / 16.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Fragment 3-(1-Methyl-2-Oxo-1,2-Dihydroquinoxalin- 3-Yl)Propionic Acid Bound in the Ubiquitin Binding Pocket of the HDAC6 Zinc-Finger Domain (pdb code 6cee). 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-(1-Methyl-2-Oxo-1,2-Dihydroquinoxalin- 3-Yl)Propionic Acid Bound in the Ubiquitin Binding Pocket of the HDAC6 Zinc-Finger Domain, PDB code: 6cee:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 6cee

Go back to Zinc Binding Sites List in 6cee
Zinc binding site 1 out of 3 in the Crystal Structure of Fragment 3-(1-Methyl-2-Oxo-1,2-Dihydroquinoxalin- 3-Yl)Propionic 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-(1-Methyl-2-Oxo-1,2-Dihydroquinoxalin- 3-Yl)Propionic 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:10.4
occ:1.00
 NE2 A:HIS1164 2.0 9.9 1.0
ND1 A:HIS1170 2.1 8.5 1.0
SG A:CYS1145 2.3 8.8 1.0
SG A:CYS1148 2.4 11.9 1.0
CE1 A:HIS1164 3.0 9.9 1.0
CE1 A:HIS1170 3.0 8.5 1.0
CD2 A:HIS1164 3.1 9.4 1.0
CG A:HIS1170 3.1 8.3 1.0
CB A:CYS1145 3.2 8.8 1.0
CB A:HIS1170 3.5 8.6 1.0
CB A:CYS1148 3.5 10.8 1.0
N A:CYS1148 3.8 9.3 1.0
ND1 A:HIS1164 4.1 10.4 1.0
NE2 A:HIS1170 4.1 9.4 1.0
CA A:CYS1148 4.2 9.5 1.0
CG A:HIS1164 4.2 8.9 1.0
CD2 A:HIS1170 4.2 8.6 1.0
OG A:SER1168 4.2 9.7 1.0
CB A:SER1147 4.4 8.8 1.0
CA A:CYS1145 4.6 8.1 1.0
C A:SER1147 4.8 9.7 1.0
CB A:SER1168 4.8 9.7 1.0
C A:CYS1148 4.8 9.7 1.0
N A:SER1147 4.9 8.5 1.0
CA A:SER1147 4.9 8.8 1.0
N A:TYR1149 4.9 9.0 1.0
CA A:HIS1170 5.0 8.3 1.0

Zinc binding site 2 out of 3 in 6cee

Go back to Zinc Binding Sites List in 6cee
Zinc binding site 2 out of 3 in the Crystal Structure of Fragment 3-(1-Methyl-2-Oxo-1,2-Dihydroquinoxalin- 3-Yl)Propionic 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-(1-Methyl-2-Oxo-1,2-Dihydroquinoxalin- 3-Yl)Propionic 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:11.2
occ:1.00
 ND1 A:HIS1160 2.1 11.2 1.0
SG A:CYS1136 2.3 10.0 1.0
SG A:CYS1153 2.3 9.2 1.0
SG A:CYS1133 2.4 10.0 1.0
CE1 A:HIS1160 3.0 11.4 1.0
CG A:HIS1160 3.1 10.4 1.0
CB A:CYS1133 3.3 9.8 1.0
CB A:CYS1153 3.4 9.1 1.0
CB A:CYS1136 3.4 12.2 1.0
CB A:HIS1160 3.5 9.8 1.0
N A:CYS1136 3.7 12.0 1.0
N A:CYS1153 4.0 8.3 1.0
CB A:ASN1158 4.1 12.3 1.0
CG2 A:THR1138 4.1 10.2 1.0
CA A:CYS1136 4.1 11.8 1.0
NE2 A:HIS1160 4.2 11.6 1.0
CD2 A:HIS1160 4.2 11.9 1.0
CA A:CYS1153 4.3 8.4 1.0
ND2 A:ASN1158 4.5 12.1 1.0
CB A:ASP1135 4.6 15.9 1.0
N A:HIS1160 4.6 9.7 1.0
CA A:HIS1160 4.7 9.5 1.0
CA A:CYS1133 4.7 9.5 1.0
C A:ASP1135 4.8 14.0 1.0
C A:CYS1136 4.8 11.6 1.0
CG A:ASN1158 4.8 12.9 1.0
CA A:ASN1158 4.9 11.2 1.0
N A:GLY1137 4.9 11.4 1.0
N A:ASN1158 5.0 10.8 1.0

Zinc binding site 3 out of 3 in 6cee

Go back to Zinc Binding Sites List in 6cee
Zinc binding site 3 out of 3 in the Crystal Structure of Fragment 3-(1-Methyl-2-Oxo-1,2-Dihydroquinoxalin- 3-Yl)Propionic 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-(1-Methyl-2-Oxo-1,2-Dihydroquinoxalin- 3-Yl)Propionic 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:9.6
occ:1.00
 ND1 A:HIS1115 2.1 9.2 1.0
SG A:CYS1113 2.3 8.2 1.0
SG A:CYS1183 2.3 7.5 1.0
SG A:CYS1186 2.3 9.5 1.0
CE1 A:HIS1115 3.1 9.1 1.0
CG A:HIS1115 3.1 8.8 1.0
CB A:CYS1113 3.3 8.5 1.0
CB A:CYS1183 3.3 7.9 1.0
CB A:CYS1186 3.4 9.9 1.0
CB A:HIS1115 3.5 8.1 1.0
N A:CYS1186 3.9 9.5 1.0
N A:HIS1115 4.0 8.6 1.0
CD A:PRO1114 4.1 10.1 1.0
NE2 A:HIS1115 4.2 9.2 1.0
CD2 A:HIS1115 4.2 9.4 1.0
CA A:CYS1186 4.3 10.1 1.0
N A:PRO1114 4.3 9.8 1.0
CA A:HIS1115 4.4 8.7 1.0
CA A:CYS1113 4.5 8.9 1.0
CB A:TYR1185 4.6 8.7 1.0
CG A:PRO1114 4.6 11.2 1.0
C A:CYS1113 4.6 9.3 1.0
CA A:CYS1183 4.7 7.6 1.0
O A:HOH1482 4.9 15.6 1.0
C A:PRO1114 4.9 9.4 1.0
C A:TYR1185 5.0 8.9 1.0

Reference:

R.Ferreira De Freitas, R.J.Harding, I.Franzoni, M.Ravichandran, M.K.Mann, H.Ouyang, M.Lautens, V.Santhakumar, C.H.Arrowsmith, M.Schapira. Identification and Structure-Activity Relationship of HDAC6 Zinc-Finger Ubiquitin Binding Domain Inhibitors. J. Med. Chem. V. 61 4517 2018.
ISSN: ISSN 1520-4804
PubMed: 29741882
DOI: 10.1021/ACS.JMEDCHEM.8B00258
Page generated: Mon Oct 28 18:45:48 2024

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