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Fluorine in PDB 6oda: Crystal Structure of HDAC8 in Complex with Compound 2

Enzymatic activity of Crystal Structure of HDAC8 in Complex with Compound 2

All present enzymatic activity of Crystal Structure of HDAC8 in Complex with Compound 2:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of HDAC8 in Complex with Compound 2, PDB code: 6oda was solved by X.Zheng, C.Conti, J.Caravella, M.-M.Zablocki, K.Bair, N.Barczak, B.Han, D.Lancia Jr., C.Liu, M.Martin, P.Y.Ng, A.Rudnitskaya, J.J.Thomason, R.Garcia-Dancey, C.Hardy, J.Lahdenranta, C.Leng, P.Li, E.Pardo, A.Saldahna, T.Tan, A.V.Toms, L.Yao, C.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.88
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 87.750, 91.290, 92.700, 90.00, 94.09, 90.00
R / Rfree (%) 19.9 / 24.9

Other elements in 6oda:

The structure of Crystal Structure of HDAC8 in Complex with Compound 2 also contains other interesting chemical elements:

Potassium (K) 6 atoms
Zinc (Zn) 3 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of HDAC8 in Complex with Compound 2 (pdb code 6oda). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 9 binding sites of Fluorine where determined in the Crystal Structure of HDAC8 in Complex with Compound 2, PDB code: 6oda:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Fluorine binding site 1 out of 9 in 6oda

Go back to Fluorine Binding Sites List in 6oda
Fluorine binding site 1 out of 9 in the Crystal Structure of HDAC8 in Complex with Compound 2


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 HDAC8 in Complex with Compound 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:0.4
occ:1.00
 FAW A:C7401 0.0 0.4 1.0
CAV A:C7401 1.3 0.9 1.0
FAY A:C7401 2.2 0.2 1.0
FAX A:C7401 2.2 0.5 1.0
CAR A:C7401 2.3 0.6 1.0
CAS A:C7401 2.8 0.8 1.0
CAQ A:C7401 3.5 0.7 1.0
CAT A:C7401 4.1 0.2 1.0
CAO A:C7401 4.7 0.4 1.0
O A:LYS33 4.7 72.6 1.0
CE A:LYS33 4.9 83.0 1.0
CAU A:C7401 4.9 0.7 1.0

Fluorine binding site 2 out of 9 in 6oda

Go back to Fluorine Binding Sites List in 6oda
Fluorine binding site 2 out of 9 in the Crystal Structure of HDAC8 in Complex with Compound 2


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 HDAC8 in Complex with Compound 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:0.5
occ:1.00
 FAX A:C7401 0.0 0.5 1.0
CAV A:C7401 1.3 0.9 1.0
FAY A:C7401 2.2 0.2 1.0
FAW A:C7401 2.2 0.4 1.0
CAR A:C7401 2.3 0.6 1.0
CAS A:C7401 2.9 0.8 1.0
CAQ A:C7401 3.3 0.7 1.0
CAT A:C7401 4.2 0.2 1.0
CAO A:C7401 4.5 0.4 1.0
CB A:PRO273 4.6 42.5 1.0
CG A:PRO273 4.8 42.4 1.0
CAU A:C7401 4.9 0.7 1.0

Fluorine binding site 3 out of 9 in 6oda

Go back to Fluorine Binding Sites List in 6oda
Fluorine binding site 3 out of 9 in the Crystal Structure of HDAC8 in Complex with Compound 2


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 HDAC8 in Complex with Compound 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:0.2
occ:1.00
 FAY A:C7401 0.0 0.2 1.0
CAV A:C7401 1.3 0.9 1.0
FAW A:C7401 2.2 0.4 1.0
FAX A:C7401 2.2 0.5 1.0
CAR A:C7401 2.4 0.6 1.0
CAQ A:C7401 2.8 0.7 1.0
CAS A:C7401 3.6 0.8 1.0
CAO A:C7401 4.2 0.4 1.0
CAT A:C7401 4.7 0.2 1.0
OAP A:C7401 4.8 0.7 1.0
CE A:LYS33 5.0 83.0 1.0
CAU A:C7401 5.0 0.7 1.0

Fluorine binding site 4 out of 9 in 6oda

Go back to Fluorine Binding Sites List in 6oda
Fluorine binding site 4 out of 9 in the Crystal Structure of HDAC8 in Complex with Compound 2


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 HDAC8 in Complex with Compound 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:0.9
occ:1.00
 FAW B:C7401 0.0 0.9 1.0
CAV B:C7401 1.3 0.9 1.0
FAY B:C7401 2.1 1.0 1.0
FAX B:C7401 2.2 0.1 1.0
CAR B:C7401 2.3 0.2 1.0
CAQ B:C7401 2.8 96.3 1.0
CAS B:C7401 3.6 92.4 1.0
CAO B:C7401 4.2 92.3 1.0
NZ B:LYS33 4.7 92.8 1.0
CAT B:C7401 4.7 91.2 1.0
OAP B:C7401 4.8 91.8 1.0
CAU B:C7401 4.9 91.4 1.0

Fluorine binding site 5 out of 9 in 6oda

Go back to Fluorine Binding Sites List in 6oda
Fluorine binding site 5 out of 9 in the Crystal Structure of HDAC8 in Complex with Compound 2


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 HDAC8 in Complex with Compound 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:0.1
occ:1.00
 FAX B:C7401 0.0 0.1 1.0
CAV B:C7401 1.3 0.9 1.0
FAW B:C7401 2.2 0.9 1.0
FAY B:C7401 2.2 1.0 1.0
CAR B:C7401 2.3 0.2 1.0
CAS B:C7401 3.1 92.4 1.0
CAQ B:C7401 3.2 96.3 1.0
NZ B:LYS33 3.9 92.8 1.0
CD B:LYS33 4.0 93.5 1.0
CAT B:C7401 4.4 91.2 1.0
CAO B:C7401 4.5 92.3 1.0
CE B:LYS33 4.5 93.5 1.0
CAU B:C7401 4.9 91.4 1.0

Fluorine binding site 6 out of 9 in 6oda

Go back to Fluorine Binding Sites List in 6oda
Fluorine binding site 6 out of 9 in the Crystal Structure of HDAC8 in Complex with Compound 2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of HDAC8 in Complex with Compound 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:1.0
occ:1.00
 FAY B:C7401 0.0 1.0 1.0
CAV B:C7401 1.3 0.9 1.0
FAW B:C7401 2.1 0.9 1.0
FAX B:C7401 2.2 0.1 1.0
CAR B:C7401 2.3 0.2 1.0
CAS B:C7401 2.7 92.4 1.0
CAQ B:C7401 3.6 96.3 1.0
CAT B:C7401 4.1 91.2 1.0
CB B:PRO273 4.4 46.1 1.0
CAO B:C7401 4.7 92.3 1.0
CG B:PRO273 4.8 46.2 1.0
CAU B:C7401 4.9 91.4 1.0

Fluorine binding site 7 out of 9 in 6oda

Go back to Fluorine Binding Sites List in 6oda
Fluorine binding site 7 out of 9 in the Crystal Structure of HDAC8 in Complex with Compound 2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of HDAC8 in Complex with Compound 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F401

b:0.7
occ:1.00
 FAW C:C7401 0.0 0.7 1.0
CAV C:C7401 1.3 0.1 1.0
FAX C:C7401 2.2 0.1 1.0
FAY C:C7401 2.2 0.3 1.0
CAR C:C7401 2.3 0.4 1.0
CAQ C:C7401 2.8 0.0 1.0
CAS C:C7401 3.5 98.9 1.0
CAO C:C7401 4.2 99.7 1.0
CAT C:C7401 4.7 99.0 1.0
NZ C:LYS33 4.8 91.1 1.0
CAU C:C7401 4.9 99.4 1.0
OAP C:C7401 4.9 98.0 1.0

Fluorine binding site 8 out of 9 in 6oda

Go back to Fluorine Binding Sites List in 6oda
Fluorine binding site 8 out of 9 in the Crystal Structure of HDAC8 in Complex with Compound 2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of HDAC8 in Complex with Compound 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F401

b:0.1
occ:1.00
 FAX C:C7401 0.0 0.1 1.0
CAV C:C7401 1.3 0.1 1.0
FAY C:C7401 2.2 0.3 1.0
FAW C:C7401 2.2 0.7 1.0
CAR C:C7401 2.3 0.4 1.0
CAS C:C7401 2.7 98.9 1.0
CAQ C:C7401 3.6 0.0 1.0
CAT C:C7401 4.1 99.0 1.0
CB C:PRO273 4.3 62.8 1.0
CAO C:C7401 4.8 99.7 1.0
CG C:PRO273 4.8 62.0 1.0
CAU C:C7401 5.0 99.4 1.0

Fluorine binding site 9 out of 9 in 6oda

Go back to Fluorine Binding Sites List in 6oda
Fluorine binding site 9 out of 9 in the Crystal Structure of HDAC8 in Complex with Compound 2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Crystal Structure of HDAC8 in Complex with Compound 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F401

b:0.3
occ:1.00
 FAY C:C7401 0.0 0.3 1.0
CAV C:C7401 1.3 0.1 1.0
FAX C:C7401 2.2 0.1 1.0
FAW C:C7401 2.2 0.7 1.0
CAR C:C7401 2.3 0.4 1.0
CAQ C:C7401 3.0 0.0 1.0
CAS C:C7401 3.3 98.9 1.0
CAO C:C7401 4.3 99.7 1.0
CB C:PRO273 4.3 62.8 1.0
CAT C:C7401 4.4 99.0 1.0
CAU C:C7401 4.9 99.4 1.0

Reference:

X.Zheng, C.Conti, J.Caravella, M.-M.Zablocki, K.Bair, N.Barczak, B.Han, D.Lancia Jr., C.Liu, M.Martin, P.Y.Ng, A.Rudnitskaya, J.J.Thomason, R.Garcia-Dancey, C.Hardy, J.Lahdenranta, C.Leng, P.Li, E.Pardo, A.Saldahna, T.Tan, A.V.Toms, L.Yao, C.Zhang. Structure-Based Discovery of Novel N-(E)-N-Hydroxy-3-(2-(2-Oxoimidazolidin-1-Yl)Phenyl) Acrylamides As Potent and Selective HDAC8 Inhibitors To Be Published.
Page generated: Tue Jul 15 14:04:38 2025

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