Fluorine in PDB 6hu3: Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Triazole Hydroxamate Inhibitor

Enzymatic activity of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Triazole Hydroxamate Inhibitor

All present enzymatic activity of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Triazole Hydroxamate Inhibitor:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Triazole Hydroxamate Inhibitor, PDB code: 6hu3 was solved by T.B.Shaik, M.Marek, C.Romier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.95 / 1.66
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 70.640, 70.430, 97.920, 75.48, 78.20, 86.17
R / Rfree (%) 16.2 / 19.4

Other elements in 6hu3:

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Triazole Hydroxamate Inhibitor also contains other interesting chemical elements:

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

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Triazole Hydroxamate Inhibitor (pdb code 6hu3). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Triazole Hydroxamate Inhibitor, PDB code: 6hu3:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 6hu3

Go back to Fluorine Binding Sites List in 6hu3
Fluorine binding site 1 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Triazole Hydroxamate 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 Schistosoma Mansoni HDAC8 Complexed with A Triazole Hydroxamate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F504

b:68.5
occ:1.00
 F1 A:GRZ504 0.0 68.5 1.0
C1 A:GRZ504 1.4 59.3 1.0
C2 A:GRZ504 2.3 57.9 1.0
C6 A:GRZ504 2.3 54.2 1.0
CG A:PRO291 3.3 39.6 1.0
C3 A:GRZ504 3.6 55.7 1.0
C5 A:GRZ504 3.6 55.2 1.0
CB A:PRO291 3.6 39.7 1.0
CB A:TYR341 4.1 35.0 1.0
C4 A:GRZ504 4.1 55.1 1.0
CG A:TYR341 4.7 45.7 1.0
CD A:PRO291 4.8 31.2 1.0
CA A:PRO291 4.9 35.9 1.0

Fluorine binding site 2 out of 4 in 6hu3

Go back to Fluorine Binding Sites List in 6hu3
Fluorine binding site 2 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Triazole Hydroxamate 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 Schistosoma Mansoni HDAC8 Complexed with A Triazole Hydroxamate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F504

b:52.1
occ:1.00
 F1 B:GRZ504 0.0 52.1 1.0
C1 B:GRZ504 1.4 57.7 1.0
C2 B:GRZ504 2.3 54.7 1.0
C6 B:GRZ504 2.4 55.8 1.0
CG B:PRO291 3.2 29.1 1.0
CB B:PRO291 3.6 30.8 1.0
C3 B:GRZ504 3.6 54.2 1.0
C5 B:GRZ504 3.6 51.6 1.0
O B:HOH837 3.9 58.0 1.0
CB B:TYR341 4.1 35.8 1.0
C4 B:GRZ504 4.1 54.5 1.0
CD B:PRO291 4.7 25.3 1.0
CG B:TYR341 4.7 42.4 1.0
NZ B:LYS20 4.8 83.9 1.0
CA B:PRO291 4.9 28.6 1.0

Fluorine binding site 3 out of 4 in 6hu3

Go back to Fluorine Binding Sites List in 6hu3
Fluorine binding site 3 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Triazole Hydroxamate 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 Schistosoma Mansoni HDAC8 Complexed with A Triazole Hydroxamate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F504

b:59.1
occ:1.00
 F1 C:GRZ504 0.0 59.1 1.0
C1 C:GRZ504 1.4 57.1 1.0
C6 C:GRZ504 2.3 55.4 1.0
C2 C:GRZ504 2.4 53.6 1.0
CG C:PRO291 3.2 31.3 1.0
CB C:PRO291 3.5 29.9 1.0
C5 C:GRZ504 3.6 55.4 1.0
C3 C:GRZ504 3.6 52.7 1.0
O C:HOH820 4.0 54.8 1.0
C4 C:GRZ504 4.1 52.3 1.0
CB C:TYR341 4.1 31.7 1.0
CD C:PRO291 4.7 28.5 1.0
CG C:TYR341 4.8 41.5 1.0
NZ C:LYS20 4.8 79.7 1.0
CA C:PRO291 4.9 28.9 1.0

Fluorine binding site 4 out of 4 in 6hu3

Go back to Fluorine Binding Sites List in 6hu3
Fluorine binding site 4 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Triazole Hydroxamate 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 Schistosoma Mansoni HDAC8 Complexed with A Triazole Hydroxamate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F504

b:74.8
occ:1.00
 F1 D:GRZ504 0.0 74.8 1.0
C1 D:GRZ504 1.4 69.8 1.0
C2 D:GRZ504 2.3 68.4 1.0
C6 D:GRZ504 2.3 70.0 1.0
CG D:PRO291 3.3 40.7 1.0
CB D:PRO291 3.4 35.5 1.0
C3 D:GRZ504 3.6 68.5 1.0
C5 D:GRZ504 3.6 69.8 1.0
C4 D:GRZ504 4.1 71.1 1.0
CB D:TYR341 4.5 37.6 1.0
O D:HOH792 4.5 59.3 1.0
CA D:PRO291 4.7 34.1 1.0
CD D:PRO291 4.8 40.1 1.0
C D:PRO291 4.9 35.5 1.0

Reference:

M.Marek, T.B.Shaik, T.Heimburg, A.Chakrabarti, J.Lancelot, E.Ramos-Morales, C.Da Veiga, D.Kalinin, J.Melesina, D.Robaa, K.Schmidtkunz, T.Suzuki, R.Holl, E.Ennifar, R.J.Pierce, M.Jung, W.Sippl, C.Romier. Characterization of Histone Deacetylase 8 (HDAC8) Selective Inhibition Reveals Specific Active Site Structural and Functional Determinants. J. Med. Chem. V. 61 10000 2018.
ISSN: ISSN 1520-4804
PubMed: 30347148
DOI: 10.1021/ACS.JMEDCHEM.8B01087
Page generated: Sun Dec 13 12:53:53 2020

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