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Zinc in PDB 5kh9: Crystal Structure of A Low Occupancy Fragment Candidate (5-[(4- Isopropylphenyl)Amino]-6-Methyl-1,2,4-Triazin-3(2H)-One) Bound in the Ubiquitin Binding Pocket of the HDAC6 Zinc-Finger Domain

Enzymatic activity of Crystal Structure of A Low Occupancy Fragment Candidate (5-[(4- Isopropylphenyl)Amino]-6-Methyl-1,2,4-Triazin-3(2H)-One) Bound in the Ubiquitin Binding Pocket of the HDAC6 Zinc-Finger Domain

All present enzymatic activity of Crystal Structure of A Low Occupancy Fragment Candidate (5-[(4- Isopropylphenyl)Amino]-6-Methyl-1,2,4-Triazin-3(2H)-One) 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 A Low Occupancy Fragment Candidate (5-[(4- Isopropylphenyl)Amino]-6-Methyl-1,2,4-Triazin-3(2H)-One) Bound in the Ubiquitin Binding Pocket of the HDAC6 Zinc-Finger Domain, PDB code: 5kh9 was solved by R.J.Harding, W.Tempel, M.Ravichandran, P.Collins, N.Pearce, J.Brandao-Neto, A.Douangamath, M.Schapira, C.Bountra, A.M.Edwards, F.Von Delft, V.Santhakumar, 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) 34.80 / 1.07
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 41.434, 44.157, 56.549, 90.00, 90.00, 90.00
R / Rfree (%) 13.6 / 15

Other elements in 5kh9:

The structure of Crystal Structure of A Low Occupancy Fragment Candidate (5-[(4- Isopropylphenyl)Amino]-6-Methyl-1,2,4-Triazin-3(2H)-One) Bound in the Ubiquitin Binding Pocket of the HDAC6 Zinc-Finger Domain also contains other interesting chemical elements:

Sodium (Na) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of A Low Occupancy Fragment Candidate (5-[(4- Isopropylphenyl)Amino]-6-Methyl-1,2,4-Triazin-3(2H)-One) Bound in the Ubiquitin Binding Pocket of the HDAC6 Zinc-Finger Domain (pdb code 5kh9). 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 A Low Occupancy Fragment Candidate (5-[(4- Isopropylphenyl)Amino]-6-Methyl-1,2,4-Triazin-3(2H)-One) Bound in the Ubiquitin Binding Pocket of the HDAC6 Zinc-Finger Domain, PDB code: 5kh9:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 5kh9

Go back to Zinc Binding Sites List in 5kh9
Zinc binding site 1 out of 3 in the Crystal Structure of A Low Occupancy Fragment Candidate (5-[(4- Isopropylphenyl)Amino]-6-Methyl-1,2,4-Triazin-3(2H)-One) 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 A Low Occupancy Fragment Candidate (5-[(4- Isopropylphenyl)Amino]-6-Methyl-1,2,4-Triazin-3(2H)-One) 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:9.8
occ:1.00
 UNK A:UNX1306 2.0 9.8 1.0
ND1 A:HIS1170 2.1 10.2 1.0
NE2 A:HIS1164 2.1 9.1 1.0
SG A:CYS1145 2.3 9.8 1.0
CE1 A:HIS1164 3.0 10.0 1.0
CE1 A:HIS1170 3.0 10.6 1.0
CG A:HIS1170 3.1 9.6 1.0
CD2 A:HIS1164 3.1 9.3 1.0
CB A:CYS1145 3.2 8.8 1.0
SG A:CYS1148 3.2 11.3 1.0
UNK A:UNX1307 3.4 11.2 1.0
CB A:HIS1170 3.4 9.2 1.0
N A:CYS1148 4.0 9.9 1.0
CB A:CYS1148 4.1 11.0 1.0
OG A:SER1168 4.2 10.5 1.0
ND1 A:HIS1164 4.2 10.8 1.0
NE2 A:HIS1170 4.2 11.7 1.0
CD2 A:HIS1170 4.2 11.1 1.0
CG A:HIS1164 4.2 9.7 1.0
CB A:SER1147 4.4 9.3 1.0
CA A:CYS1148 4.5 10.2 1.0
CA A:CYS1145 4.6 8.2 1.0
UNK A:UNX1326 4.6 18.2 1.0
CB A:SER1168 4.8 10.8 1.0
C A:SER1147 4.9 10.5 1.0
O A:HOH1477 4.9 28.7 1.0
CA A:HIS1170 4.9 9.3 1.0
N A:SER1147 5.0 8.8 1.0
CA A:SER1147 5.0 9.4 1.0

Zinc binding site 2 out of 3 in 5kh9

Go back to Zinc Binding Sites List in 5kh9
Zinc binding site 2 out of 3 in the Crystal Structure of A Low Occupancy Fragment Candidate (5-[(4- Isopropylphenyl)Amino]-6-Methyl-1,2,4-Triazin-3(2H)-One) 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 A Low Occupancy Fragment Candidate (5-[(4- Isopropylphenyl)Amino]-6-Methyl-1,2,4-Triazin-3(2H)-One) 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:10.5
occ:1.00
 ND1 A:HIS1160 2.1 10.9 1.0
SG A:CYS1136 2.4 11.5 1.0
SG A:CYS1153 2.4 10.0 1.0
SG A:CYS1133 2.4 10.0 1.0
CE1 A:HIS1160 3.1 11.7 1.0
CG A:HIS1160 3.1 10.9 1.0
CB A:CYS1133 3.3 9.7 1.0
CB A:CYS1153 3.4 9.4 1.0
CB A:HIS1160 3.5 10.0 1.0
CB A:CYS1136 3.5 12.4 1.0
N A:CYS1136 3.8 12.2 1.0
N A:CYS1153 4.0 8.8 1.0
CB A:ASN1158 4.1 13.5 1.0
CA A:CYS1136 4.2 12.9 1.0
CG2 A:THR1138 4.2 11.0 1.0
NE2 A:HIS1160 4.2 13.2 1.0
CD2 A:HIS1160 4.3 13.1 1.0
CA A:CYS1153 4.3 8.8 1.0
ND2 A:ASN1158 4.5 16.0 1.0
CB A:ASP1135 4.6 14.1 0.5
CB A:ASP1135 4.6 13.3 0.5
N A:HIS1160 4.6 10.1 1.0
CA A:HIS1160 4.7 10.0 1.0
CA A:CYS1133 4.8 9.8 1.0
C A:ASP1135 4.9 10.0 0.5
CG A:ASN1158 4.9 14.8 1.0
C A:CYS1136 4.9 12.1 1.0
CA A:ASN1158 5.0 12.4 1.0
N A:GLY1137 5.0 11.9 1.0

Zinc binding site 3 out of 3 in 5kh9

Go back to Zinc Binding Sites List in 5kh9
Zinc binding site 3 out of 3 in the Crystal Structure of A Low Occupancy Fragment Candidate (5-[(4- Isopropylphenyl)Amino]-6-Methyl-1,2,4-Triazin-3(2H)-One) 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 A Low Occupancy Fragment Candidate (5-[(4- Isopropylphenyl)Amino]-6-Methyl-1,2,4-Triazin-3(2H)-One) 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:11.9
occ:1.00
 ND1 A:HIS1115 2.1 11.6 1.0
SG A:CYS1183 2.3 10.3 1.0
SG A:CYS1113 2.3 11.4 1.0
SG A:CYS1186 2.5 16.5 1.0
CE1 A:HIS1115 3.1 12.8 1.0
CG A:HIS1115 3.2 11.4 1.0
CB A:CYS1113 3.3 12.6 1.0
CB A:CYS1183 3.3 9.3 1.0
CB A:CYS1186 3.6 13.0 1.0
CB A:HIS1115 3.6 11.5 1.0
N A:CYS1186 4.0 11.7 1.0
N A:HIS1115 4.0 12.0 1.0
NE2 A:HIS1115 4.2 13.6 1.0
CD A:PRO1114 4.2 14.9 1.0
CD2 A:HIS1115 4.3 13.2 1.0
CA A:CYS1186 4.4 12.2 1.0
N A:PRO1114 4.4 13.8 1.0
CA A:HIS1115 4.4 12.0 1.0
CB A:TYR1185 4.5 11.0 1.0
CA A:CYS1113 4.5 13.0 1.0
C A:CYS1113 4.6 12.7 1.0
CA A:CYS1183 4.8 9.0 1.0
CG A:PRO1114 4.8 17.8 1.0
C A:TYR1185 5.0 12.3 1.0
C A:PRO1114 5.0 13.6 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 20:24:54 2024

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