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Fluorine in PDB 7u8z: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (CD2) Complexed with Fluorinated Peptoid Inhibitor

Protein crystallography data

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (CD2) Complexed with Fluorinated Peptoid Inhibitor, PDB code: 7u8z was solved by P.R.Watson, A.D.Cragin, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 56.48 / 1.85
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 78.34, 95.13, 98.139, 90, 98.73, 90
R / Rfree (%) 17.2 / 21.5

Other elements in 7u8z:

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (CD2) Complexed with Fluorinated Peptoid Inhibitor also contains other interesting chemical elements:

Potassium (K) 8 atoms
Zinc (Zn) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (CD2) Complexed with Fluorinated Peptoid Inhibitor (pdb code 7u8z). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 5 binding sites of Fluorine where determined in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (CD2) Complexed with Fluorinated Peptoid Inhibitor, PDB code: 7u8z:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5;

Fluorine binding site 1 out of 5 in 7u8z

Go back to Fluorine Binding Sites List in 7u8z
Fluorine binding site 1 out of 5 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (CD2) Complexed with Fluorinated Peptoid Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (CD2) Complexed with Fluorinated Peptoid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F902

b:17.7
occ:1.00
 F18 A:M0I902 0.0 17.7 1.0
C17 A:M0I902 1.4 9.1 1.0
C16 A:M0I902 2.4 11.1 1.0
C19 A:M0I902 2.4 7.0 1.0
C15 A:M0I902 2.8 6.9 1.0
CB A:SER531 3.1 6.1 1.0
CA A:GLY582 3.1 11.6 1.0
CZ A:PHE643 3.3 7.7 1.0
OG A:SER531 3.4 7.6 1.0
CE1 A:PHE643 3.4 7.6 1.0
C26 A:M0I902 3.6 16.3 1.0
C20 A:M0I902 3.7 7.4 1.0
CE1 A:PHE583 3.7 7.5 1.0
C A:GLY582 3.8 9.3 1.0
CE2 A:PHE643 3.9 9.4 1.0
CZ A:PHE583 4.0 9.4 1.0
N03 A:M0I902 4.0 12.0 1.0
CD1 A:PHE583 4.0 9.1 1.0
CD1 A:PHE643 4.1 6.0 1.0
C25 A:M0I902 4.1 9.5 1.0
N A:GLY582 4.1 9.7 1.0
O A:GLY582 4.2 13.4 1.0
C04 A:M0I902 4.2 11.5 1.0
O A:SER531 4.3 7.5 1.0
N A:PHE583 4.4 7.1 1.0
CD2 A:PHE643 4.4 8.8 1.0
CE2 A:PHE583 4.5 12.9 1.0
CG A:PHE583 4.5 9.4 1.0
CA A:SER531 4.5 8.4 1.0
CG A:PHE643 4.5 9.9 1.0
CD2 A:PHE583 4.7 7.8 1.0
C A:SER531 4.9 9.1 1.0
C21 A:M0I902 5.0 13.4 1.0
O A:HOH1167 5.0 10.4 1.0

Fluorine binding site 2 out of 5 in 7u8z

Go back to Fluorine Binding Sites List in 7u8z
Fluorine binding site 2 out of 5 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (CD2) Complexed with Fluorinated Peptoid Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (CD2) Complexed with Fluorinated Peptoid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:9.1
occ:0.22
 F18 B:M0I801 0.0 9.1 0.2
C26 B:M0I801 1.3 8.8 0.7
C17 B:M0I801 1.4 9.0 0.2
C16 B:M0I801 2.3 9.3 0.7
C25 B:M0I801 2.3 11.0 0.7
C19 B:M0I801 2.4 10.8 0.2
C16 B:M0I801 2.4 9.4 0.2
C15 B:M0I801 2.7 10.2 0.7
N03 B:M0I801 2.8 11.2 0.7
C15 B:M0I801 2.8 10.2 0.2
N03 B:M0I801 2.9 11.2 0.2
C02 B:M0I801 3.0 11.3 0.7
C02 B:M0I801 3.0 11.1 0.2
CD2 B:LEU712 3.2 13.6 1.0
C27 B:M0I801 3.2 9.0 0.7
C27 B:M0I801 3.2 9.2 0.2
C35 B:M0I801 3.4 10.4 0.2
C35 B:M0I801 3.4 10.5 0.7
C17 B:M0I801 3.5 8.3 0.7
C20 B:M0I801 3.6 9.5 0.7
C20 B:M0I801 3.6 9.6 0.2
C26 B:M0I801 3.7 8.4 0.2
C04 B:M0I801 3.7 11.0 0.7
O01 B:M0I801 3.7 11.8 0.7
C04 B:M0I801 3.8 11.0 0.2
O01 B:M0I801 3.8 11.8 0.2
CZ B:PHE583 3.8 10.4 1.0
C28 B:M0I801 4.0 8.7 0.7
C19 B:M0I801 4.0 9.5 0.7
C28 B:M0I801 4.0 8.9 0.2
CE2 B:PHE583 4.1 13.4 1.0
C25 B:M0I801 4.1 9.6 0.2
CG B:LEU712 4.3 10.9 1.0
CD1 B:LEU712 4.3 13.3 1.0
C34 B:M0I801 4.3 9.2 0.2
O B:HOH1040 4.3 16.3 1.0
C34 B:M0I801 4.4 9.0 0.7
F18 B:M0I801 4.6 8.3 0.7
C29 B:M0I801 4.8 11.2 0.7
C29 B:M0I801 4.8 11.1 0.2
C21 B:M0I801 4.8 12.1 0.7
C21 B:M0I801 4.9 12.0 0.2
CE1 B:PHE583 4.9 10.8 1.0
CB B:LEU712 4.9 11.2 1.0
C30 B:M0I801 4.9 10.7 0.7
C30 B:M0I801 4.9 10.7 0.2

Fluorine binding site 3 out of 5 in 7u8z

Go back to Fluorine Binding Sites List in 7u8z
Fluorine binding site 3 out of 5 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (CD2) Complexed with Fluorinated Peptoid Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (CD2) Complexed with Fluorinated Peptoid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:8.3
occ:0.71
 F18 B:M0I801 0.0 8.3 0.7
C26 B:M0I801 1.3 8.4 0.2
C17 B:M0I801 1.4 8.3 0.7
C16 B:M0I801 2.2 9.4 0.2
C16 B:M0I801 2.3 9.3 0.7
C25 B:M0I801 2.4 9.6 0.2
C19 B:M0I801 2.4 9.5 0.7
C15 B:M0I801 2.7 10.2 0.2
C15 B:M0I801 2.8 10.2 0.7
CZ B:PHE643 3.1 13.6 1.0
CB B:SER531 3.2 9.0 1.0
CA B:GLY582 3.3 7.7 1.0
CE1 B:PHE643 3.3 9.3 1.0
OG B:SER531 3.4 12.9 1.0
C17 B:M0I801 3.5 9.0 0.2
CE2 B:PHE643 3.5 9.2 1.0
C20 B:M0I801 3.6 9.6 0.2
C26 B:M0I801 3.6 8.8 0.7
C20 B:M0I801 3.7 9.5 0.7
N03 B:M0I801 3.7 11.2 0.2
N03 B:M0I801 3.9 11.2 0.7
CE1 B:PHE583 3.9 10.8 1.0
CD1 B:PHE643 3.9 10.7 1.0
C04 B:M0I801 3.9 11.0 0.2
C B:GLY582 3.9 9.1 1.0
C04 B:M0I801 4.0 11.0 0.7
C19 B:M0I801 4.0 10.8 0.2
CD2 B:PHE643 4.1 7.1 1.0
CZ B:PHE583 4.1 10.4 1.0
C25 B:M0I801 4.1 11.0 0.7
CD1 B:PHE583 4.2 11.5 1.0
CG B:PHE643 4.3 10.3 1.0
O B:GLY582 4.3 12.5 1.0
N B:GLY582 4.4 7.4 1.0
O B:SER531 4.5 10.4 1.0
F18 B:M0I801 4.6 9.1 0.2
CE2 B:PHE583 4.6 13.4 1.0
N B:PHE583 4.7 8.2 1.0
CA B:SER531 4.7 9.2 1.0
O B:HOH989 4.7 12.8 1.0
CG B:PHE583 4.8 7.0 1.0
CD2 B:PHE583 4.9 12.8 1.0
C21 B:M0I801 4.9 12.0 0.2
C21 B:M0I801 4.9 12.1 0.7
C05 B:M0I801 5.0 12.0 0.2

Fluorine binding site 4 out of 5 in 7u8z

Go back to Fluorine Binding Sites List in 7u8z
Fluorine binding site 4 out of 5 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (CD2) Complexed with Fluorinated Peptoid Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (CD2) Complexed with Fluorinated Peptoid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F801

b:22.0
occ:1.00
 F18 C:M0I801 0.0 22.0 1.0
C17 C:M0I801 1.3 9.5 1.0
C19 C:M0I801 2.3 9.5 1.0
C16 C:M0I801 2.4 10.1 1.0
C15 C:M0I801 2.8 10.6 1.0
CB C:SER531 2.9 11.3 1.0
CA C:GLY582 3.1 8.2 1.0
CZ C:PHE643 3.1 11.2 1.0
OG C:SER531 3.3 13.1 1.0
CE1 C:PHE643 3.4 8.1 1.0
CE2 C:PHE643 3.5 11.4 1.0
C20 C:M0I801 3.6 11.6 1.0
C26 C:M0I801 3.6 13.0 1.0
C C:GLY582 3.9 5.5 1.0
N03 C:M0I801 4.0 14.1 1.0
CD1 C:PHE643 4.0 15.8 1.0
CE1 C:PHE583 4.1 5.4 1.0
C25 C:M0I801 4.1 13.7 1.0
CD2 C:PHE643 4.1 10.5 1.0
N C:GLY582 4.1 7.8 1.0
C04 C:M0I801 4.2 11.2 1.0
O C:SER531 4.3 9.2 1.0
CZ C:PHE583 4.3 8.5 1.0
O C:GLY582 4.3 8.4 1.0
CG C:PHE643 4.3 11.0 1.0
CD1 C:PHE583 4.4 5.3 1.0
CA C:SER531 4.4 8.8 1.0
N C:PHE583 4.6 9.4 1.0
CE2 C:PHE583 4.7 12.8 1.0
O C:HOH931 4.7 9.7 1.0
C C:SER531 4.8 8.1 1.0
C21 C:M0I801 4.8 16.2 1.0
CG C:PHE583 4.8 6.8 1.0
CD2 C:PHE583 5.0 8.7 1.0

Fluorine binding site 5 out of 5 in 7u8z

Go back to Fluorine Binding Sites List in 7u8z
Fluorine binding site 5 out of 5 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (CD2) Complexed with Fluorinated Peptoid Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (CD2) Complexed with Fluorinated Peptoid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F801

b:22.8
occ:1.00
 F18 D:M0I801 0.0 22.8 1.0
C17 D:M0I801 1.4 12.6 1.0
C16 D:M0I801 2.4 9.7 1.0
C19 D:M0I801 2.4 7.8 1.0
C15 D:M0I801 2.8 10.9 1.0
CB D:SER531 3.0 10.1 1.0
CZ D:PHE643 3.2 9.5 1.0
CA D:GLY582 3.2 9.8 1.0
OG D:SER531 3.4 10.1 1.0
CE1 D:PHE643 3.4 8.3 1.0
CE2 D:PHE643 3.6 9.3 1.0
C20 D:M0I801 3.6 7.0 1.0
C26 D:M0I801 3.6 11.3 1.0
C D:GLY582 3.9 6.9 1.0
N03 D:M0I801 3.9 14.4 1.0
CE1 D:PHE583 4.0 9.1 1.0
CD1 D:PHE643 4.0 7.3 1.0
C04 D:M0I801 4.1 11.1 1.0
C25 D:M0I801 4.1 7.1 1.0
CD2 D:PHE643 4.2 9.9 1.0
CZ D:PHE583 4.2 10.6 1.0
CD1 D:PHE583 4.3 6.2 1.0
O D:SER531 4.3 8.6 1.0
N D:GLY582 4.3 9.2 1.0
O D:GLY582 4.4 10.8 1.0
CG D:PHE643 4.4 7.0 1.0
CA D:SER531 4.5 12.3 1.0
N D:PHE583 4.5 2.7 1.0
CE2 D:PHE583 4.6 12.6 1.0
CG D:PHE583 4.7 10.1 1.0
O D:HOH931 4.8 12.7 1.0
C21 D:M0I801 4.8 18.4 1.0
CD2 D:PHE583 4.8 11.0 1.0
C D:SER531 4.9 7.8 1.0
O24 D:M0I801 5.0 31.6 1.0

Reference:

N.Ressing, J.Schliehe-Diecks, P.R.Watson, M.Sonnichsen, A.D.Cragin, A.Scholer, J.Yang, L.Schaker-Hubner, A.Borkhardt, D.W.Christianson, S.Bhatia, F.K.Hansen. Development of Fluorinated Peptoid-Based Histone Deacetylase (Hdac) Inhibitors For Therapy-Resistant Acute Leukemia. J.Med.Chem. V. 65 15457 2022.
ISSN: ISSN 0022-2623
PubMed: 36351184
DOI: 10.1021/ACS.JMEDCHEM.2C01418
Page generated: Wed Jul 16 00:52:16 2025

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