Atomistry » Fluorine » PDB 7u1m-7uca » 7u8z
Atomistry »
  Fluorine »
    PDB 7u1m-7uca »
      7u8z »

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: Fri Aug 2 13:56:32 2024

Last articles

Zn in 2YRC
Zn in 2YQP
Zn in 2YR2
Zn in 2YQL
Zn in 2YPT
Zn in 2YPA
Zn in 2YPU
Zn in 2YNW
Zn in 2YNT
Zn in 2YNV
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy