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Zinc in PDB 6ced: Crystal Structure of Fragment 3-(3-Methyl-4-Oxo-3,4-Dihydroquinazolin- 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-Methyl-4-Oxo-3,4-Dihydroquinazolin- 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-Methyl-4-Oxo-3,4-Dihydroquinazolin- 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-Methyl-4-Oxo-3,4-Dihydroquinazolin- 2-Yl)Propanoic Acid Bound in the Ubiquitin Binding Pocket of the HDAC6 Zinc-Finger Domain, PDB code: 6ced 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) 34.74 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 40.720, 44.430, 55.710, 90.00, 90.00, 90.00
R / Rfree (%) 15.3 / 19.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Fragment 3-(3-Methyl-4-Oxo-3,4-Dihydroquinazolin- 2-Yl)Propanoic Acid Bound in the Ubiquitin Binding Pocket of the HDAC6 Zinc-Finger Domain (pdb code 6ced). 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-Methyl-4-Oxo-3,4-Dihydroquinazolin- 2-Yl)Propanoic Acid Bound in the Ubiquitin Binding Pocket of the HDAC6 Zinc-Finger Domain, PDB code: 6ced:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 6ced

Go back to Zinc Binding Sites List in 6ced
Zinc binding site 1 out of 3 in the Crystal Structure of Fragment 3-(3-Methyl-4-Oxo-3,4-Dihydroquinazolin- 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-Methyl-4-Oxo-3,4-Dihydroquinazolin- 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:17.3
occ:1.00
 ND1 A:HIS1170 2.1 14.0 1.0
NE2 A:HIS1164 2.1 15.0 1.0
SG A:CYS1145 2.4 14.8 1.0
SG A:CYS1148 2.7 20.6 1.0
CE1 A:HIS1170 3.0 16.0 1.0
CE1 A:HIS1164 3.1 16.9 1.0
CD2 A:HIS1164 3.1 14.5 1.0
CG A:HIS1170 3.1 13.6 1.0
CB A:CYS1145 3.2 14.7 1.0
CB A:HIS1170 3.4 13.9 1.0
CB A:CYS1148 3.9 16.3 1.0
N A:CYS1148 3.9 14.8 1.0
OG A:SER1168 4.1 14.5 1.0
NE2 A:HIS1170 4.2 15.2 1.0
ND1 A:HIS1164 4.2 15.8 1.0
CD2 A:HIS1170 4.2 13.9 1.0
CG A:HIS1164 4.2 14.5 1.0
CA A:CYS1148 4.4 14.6 1.0
CB A:SER1147 4.5 15.0 1.0
O A:HOH1439 4.6 33.4 1.0
CA A:CYS1145 4.6 12.7 1.0
CB A:SER1168 4.7 15.7 1.0
C A:SER1147 4.9 15.3 1.0
CA A:HIS1170 4.9 12.7 1.0
N A:SER1147 5.0 13.2 1.0

Zinc binding site 2 out of 3 in 6ced

Go back to Zinc Binding Sites List in 6ced
Zinc binding site 2 out of 3 in the Crystal Structure of Fragment 3-(3-Methyl-4-Oxo-3,4-Dihydroquinazolin- 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-Methyl-4-Oxo-3,4-Dihydroquinazolin- 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:17.5
occ:1.00
 ND1 A:HIS1160 2.1 17.3 1.0
SG A:CYS1136 2.3 16.5 1.0
SG A:CYS1153 2.3 14.6 1.0
SG A:CYS1133 2.3 14.8 1.0
CE1 A:HIS1160 3.1 19.3 1.0
CG A:HIS1160 3.1 16.4 1.0
CB A:CYS1133 3.3 14.3 1.0
CB A:CYS1153 3.4 14.2 1.0
CB A:CYS1136 3.4 18.9 1.0
CB A:HIS1160 3.4 15.0 1.0
N A:CYS1136 3.7 18.4 1.0
N A:CYS1153 4.0 12.4 1.0
CB A:ASN1158 4.1 20.6 1.0
CA A:CYS1136 4.1 18.7 1.0
CG2 A:THR1138 4.1 18.9 1.0
NE2 A:HIS1160 4.2 18.3 1.0
CD2 A:HIS1160 4.2 18.9 1.0
CA A:CYS1153 4.3 12.8 1.0
ND2 A:ASN1158 4.5 19.6 1.0
N A:HIS1160 4.6 13.8 1.0
CB A:ASP1135 4.6 23.1 0.7
CB A:ASP1135 4.6 18.0 0.3
CA A:HIS1160 4.6 13.5 1.0
CA A:CYS1133 4.7 14.8 1.0
C A:ASP1135 4.8 18.8 0.3
C A:CYS1136 4.8 18.6 1.0
CG A:ASN1158 4.8 21.8 1.0
C A:ASP1135 4.8 20.9 0.7
N A:GLY1137 4.9 17.9 1.0
CA A:ASN1158 4.9 17.9 1.0
N A:ASN1158 5.0 16.5 1.0

Zinc binding site 3 out of 3 in 6ced

Go back to Zinc Binding Sites List in 6ced
Zinc binding site 3 out of 3 in the Crystal Structure of Fragment 3-(3-Methyl-4-Oxo-3,4-Dihydroquinazolin- 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-Methyl-4-Oxo-3,4-Dihydroquinazolin- 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:16.5
occ:1.00
 ND1 A:HIS1115 2.1 15.4 1.0
SG A:CYS1113 2.3 14.9 1.0
SG A:CYS1183 2.3 12.8 1.0
SG A:CYS1186 2.4 18.6 1.0
CE1 A:HIS1115 3.0 17.5 1.0
CG A:HIS1115 3.1 16.3 1.0
CB A:CYS1113 3.3 15.8 1.0
CB A:CYS1183 3.3 13.6 1.0
CB A:CYS1186 3.4 16.8 1.0
CB A:HIS1115 3.5 14.9 1.0
N A:HIS1115 3.9 15.1 1.0
N A:CYS1186 4.0 16.3 1.0
CD A:PRO1114 4.1 17.6 1.0
NE2 A:HIS1115 4.2 17.3 1.0
CD2 A:HIS1115 4.2 17.6 1.0
CA A:CYS1186 4.3 17.2 1.0
CA A:HIS1115 4.4 17.8 1.0
N A:PRO1114 4.4 15.9 1.0
CA A:CYS1113 4.5 16.1 1.0
CB A:TYR1185 4.5 16.1 1.0
C A:CYS1113 4.6 16.0 1.0
CG A:PRO1114 4.7 21.2 1.0
CA A:CYS1183 4.8 13.2 1.0
O A:HOH1468 4.9 22.4 1.0
C A:PRO1114 4.9 18.2 1.0
C A:TYR1185 4.9 17.4 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 18:44:44 2024

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