Atomistry » Zinc » PDB 6c6t-6cee » 6cea
Atomistry »
  Zinc »
    PDB 6c6t-6cee »
      6cea »

Zinc in PDB 6cea: Crystal Structure of Fragment 3-(Quinolin-2-Yl)Propanoic Acid Bound in the Ubiquitin Binding Pocket of the HDAC6 Zinc-Finger Domain

Enzymatic activity of Crystal Structure of Fragment 3-(Quinolin-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-(Quinolin-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-(Quinolin-2-Yl)Propanoic Acid Bound in the Ubiquitin Binding Pocket of the HDAC6 Zinc-Finger Domain, PDB code: 6cea was solved by R.J.Harding, L.Halabelian, R.Ferreira De Freitas, M.Ravichandran, 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) 32.90 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 40.680, 44.220, 55.960, 90.00, 90.00, 90.00
R / Rfree (%) 16.4 / 19.8

Zinc Binding Sites:

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

Zinc binding site 1 out of 3 in 6cea

Go back to Zinc Binding Sites List in 6cea
Zinc binding site 1 out of 3 in the Crystal Structure of Fragment 3-(Quinolin-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-(Quinolin-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:8.8
occ:1.00
 NE2 A:HIS1164 2.0 8.9 1.0
ND1 A:HIS1170 2.1 7.3 1.0
SG A:CYS1148 2.3 8.6 1.0
SG A:CYS1145 2.3 7.4 1.0
CE1 A:HIS1164 2.9 7.8 1.0
CE1 A:HIS1170 3.0 7.7 1.0
CG A:HIS1170 3.1 7.4 1.0
CD2 A:HIS1164 3.1 7.5 1.0
CB A:CYS1145 3.2 6.9 1.0
CB A:CYS1148 3.4 8.6 1.0
CB A:HIS1170 3.5 6.9 1.0
N A:CYS1148 3.7 8.5 1.0
ND1 A:HIS1164 4.1 8.6 1.0
CA A:CYS1148 4.1 8.3 1.0
NE2 A:HIS1170 4.2 7.7 1.0
CG A:HIS1164 4.2 7.8 1.0
CD2 A:HIS1170 4.2 8.0 1.0
OG A:SER1168 4.3 9.2 1.0
CB A:SER1147 4.6 6.4 1.0
CA A:CYS1145 4.6 7.0 1.0
C A:SER1147 4.7 8.3 1.0
C A:CYS1148 4.8 8.5 1.0
CB A:SER1168 4.8 8.7 1.0
N A:TYR1149 4.9 7.3 1.0
CA A:SER1147 4.9 7.3 1.0
N A:SER1147 4.9 7.5 1.0

Zinc binding site 2 out of 3 in 6cea

Go back to Zinc Binding Sites List in 6cea
Zinc binding site 2 out of 3 in the Crystal Structure of Fragment 3-(Quinolin-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-(Quinolin-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:9.7
occ:1.00
 ND1 A:HIS1160 2.1 9.5 1.0
SG A:CYS1136 2.3 8.4 1.0
SG A:CYS1153 2.3 7.9 1.0
SG A:CYS1133 2.4 7.3 1.0
CE1 A:HIS1160 3.0 9.6 1.0
CG A:HIS1160 3.1 9.6 1.0
CB A:CYS1133 3.3 8.3 1.0
CB A:CYS1153 3.4 7.3 1.0
CB A:CYS1136 3.4 9.0 1.0
CB A:HIS1160 3.5 9.4 1.0
N A:CYS1136 3.7 10.2 1.0
N A:CYS1153 4.0 6.4 1.0
CB A:ASN1158 4.1 11.0 1.0
CA A:CYS1136 4.1 9.2 1.0
CG2 A:THR1138 4.2 9.8 1.0
NE2 A:HIS1160 4.2 10.0 1.0
CD2 A:HIS1160 4.2 10.7 1.0
CA A:CYS1153 4.3 7.0 1.0
ND2 A:ASN1158 4.4 12.0 1.0
CB A:ASP1135 4.6 11.7 0.7
N A:HIS1160 4.6 8.7 1.0
CB A:ASP1135 4.6 10.5 0.3
CA A:HIS1160 4.7 9.0 1.0
CA A:CYS1133 4.7 8.2 1.0
C A:ASP1135 4.7 10.4 0.3
CG A:ASN1158 4.8 11.9 1.0
C A:ASP1135 4.8 10.3 0.7
C A:CYS1136 4.9 9.1 1.0
CA A:ASN1158 4.9 9.6 1.0
N A:GLY1137 4.9 9.2 1.0
N A:ASN1158 5.0 9.3 1.0
N A:ASP1135 5.0 10.2 0.3
C A:ASN1158 5.0 9.7 1.0

Zinc binding site 3 out of 3 in 6cea

Go back to Zinc Binding Sites List in 6cea
Zinc binding site 3 out of 3 in the Crystal Structure of Fragment 3-(Quinolin-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-(Quinolin-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:8.3
occ:1.00
 ND1 A:HIS1115 2.1 7.6 1.0
SG A:CYS1186 2.3 7.6 1.0
SG A:CYS1183 2.3 6.0 1.0
SG A:CYS1113 2.3 7.4 1.0
CE1 A:HIS1115 3.1 8.2 1.0
CG A:HIS1115 3.1 7.7 1.0
CB A:CYS1113 3.3 8.0 1.0
CB A:CYS1186 3.3 7.6 1.0
CB A:CYS1183 3.3 6.7 1.0
CB A:HIS1115 3.5 8.0 1.0
N A:CYS1186 3.8 7.7 1.0
N A:HIS1115 4.0 8.8 1.0
CD A:PRO1114 4.1 9.5 1.0
NE2 A:HIS1115 4.2 7.7 1.0
CD2 A:HIS1115 4.2 7.7 1.0
CA A:CYS1186 4.2 7.4 1.0
N A:PRO1114 4.3 8.4 1.0
CA A:HIS1115 4.3 8.5 1.0
CA A:CYS1113 4.5 7.5 1.0
CB A:TYR1185 4.6 7.9 1.0
C A:CYS1113 4.6 7.9 1.0
CG A:PRO1114 4.6 9.6 1.0
CA A:CYS1183 4.8 7.0 1.0
C A:TYR1185 4.9 7.7 1.0
O A:HOH1485 4.9 13.8 1.0
C A:PRO1114 4.9 8.8 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 18:43:48 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy