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Fluorine in PDB 8s99: Crystal Structure of the TYK2 Pseudokinase Domain in Complex with Compound 11

Enzymatic activity of Crystal Structure of the TYK2 Pseudokinase Domain in Complex with Compound 11

All present enzymatic activity of Crystal Structure of the TYK2 Pseudokinase Domain in Complex with Compound 11:
2.7.10.2;

Protein crystallography data

The structure of Crystal Structure of the TYK2 Pseudokinase Domain in Complex with Compound 11, PDB code: 8s99 was solved by A.V.Toms, S.Leit, J.R.Greenwood, S.Carriero, S.Mondal, R.Abel, M.Ashwell, H.Blanchette, N.Boyles, M.Cartwright, A.Collis, S.Feng, P.Ghanakota, G.C.Harriman, V.Hosagrahara, N.Kaila, R.Kapeller, S.Rafi, D.L.Romero, P.Tarantino, J.Timaniya, R.T.Wester, W.Westlin, B.Srivastava, W.Miao, P.Tummino, J.J.Mcelwee, S.D.Edmondson, C.E.Massee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.62 / 1.71
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 48.209, 112.715, 157.448, 90, 90, 90
R / Rfree (%) 19 / 22.5

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of the TYK2 Pseudokinase Domain in Complex with Compound 11 (pdb code 8s99). 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 the TYK2 Pseudokinase Domain in Complex with Compound 11, PDB code: 8s99:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Fluorine binding site 1 out of 9 in 8s99

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Fluorine binding site 1 out of 9 in the Crystal Structure of the TYK2 Pseudokinase Domain in Complex with Compound 11


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 the TYK2 Pseudokinase Domain in Complex with Compound 11 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:15.0
occ:0.50
 F31 A:ZS3901 0.0 15.0 0.5
C30 A:ZS3901 1.4 14.1 0.5
C29 A:ZS3901 1.5 14.4 0.5
C28 A:ZS3901 2.4 14.1 0.5
C29 A:ZS3901 2.4 13.8 0.5
C28 A:ZS3901 2.5 13.8 0.5
N27 A:ZS3901 2.5 13.5 0.5
N27 A:ZS3901 2.7 12.9 0.5
C30 A:ZS3901 2.8 14.3 0.5
F31 A:ZS3901 3.2 15.7 0.5
C11 A:ZS3901 3.3 15.7 1.0
O A:ARG738 3.3 13.6 1.0
C10 A:ZS3901 3.4 16.5 1.0
CG A:PRO694 3.5 13.8 1.0
CD A:ARG738 3.5 15.6 1.0
N24 A:ZS3901 3.7 12.9 1.0
C25 A:ZS3901 3.8 12.9 0.5
C25 A:ZS3901 3.9 13.2 0.5
C12 A:ZS3901 3.9 15.4 1.0
CG A:ARG738 4.0 15.2 1.0
C9 A:ZS3901 4.1 16.8 1.0
CB A:PRO694 4.2 13.4 1.0
C23 A:ZS3901 4.4 12.8 1.0
CD2 A:LEU741 4.4 14.3 1.0
O A:HOH1062 4.4 21.1 1.0
C A:ARG738 4.4 13.7 1.0
C22 A:ZS3901 4.5 12.7 1.0
C14 A:ZS3901 4.5 13.4 1.0
C32 A:ZS3901 4.6 16.5 1.0
N13 A:ZS3901 4.6 13.9 1.0
O26 A:ZS3901 4.6 12.5 0.5
N8 A:ZS3901 4.6 17.6 1.0
CD A:PRO694 4.7 13.9 1.0
O26 A:ZS3901 4.7 12.9 0.5
OD1 A:ASN739 4.8 15.1 1.0
NE A:ARG738 4.9 16.4 1.0

Fluorine binding site 2 out of 9 in 8s99

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Fluorine binding site 2 out of 9 in the Crystal Structure of the TYK2 Pseudokinase Domain in Complex with Compound 11


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 the TYK2 Pseudokinase Domain in Complex with Compound 11 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:15.7
occ:0.50
 F31 A:ZS3901 0.0 15.7 0.5
C30 A:ZS3901 1.3 14.3 0.5
C28 A:ZS3901 1.5 13.8 0.5
C30 A:ZS3901 2.1 14.1 0.5
C28 A:ZS3901 2.4 14.1 0.5
C29 A:ZS3901 2.4 14.4 0.5
N27 A:ZS3901 2.5 12.9 0.5
C29 A:ZS3901 2.7 13.8 0.5
N27 A:ZS3901 2.9 13.5 0.5
F31 A:ZS3901 3.2 15.0 0.5
CG2 A:VAL603 3.2 12.7 1.0
C25 A:ZS3901 3.6 12.9 0.5
C10 A:ZS3901 3.6 16.5 1.0
C25 A:ZS3901 3.6 13.2 0.5
CE A:LYS642 3.7 12.0 1.0
NZ A:LYS642 3.7 12.3 1.0
O A:HOH1043 3.7 28.4 1.0
C11 A:ZS3901 3.8 15.7 1.0
O26 A:ZS3901 4.0 12.5 0.5
O26 A:ZS3901 4.0 12.9 0.5
CG1 A:VAL603 4.1 12.2 1.0
CB A:VAL603 4.1 12.4 1.0
CD A:LYS642 4.3 12.2 1.0
N24 A:ZS3901 4.6 12.9 1.0
C22 A:ZS3901 4.7 12.7 1.0
O A:HOH1205 4.8 52.2 1.0
C9 A:ZS3901 4.8 16.8 1.0
O A:HOH1168 4.9 22.3 1.0
O A:HOH1062 4.9 21.1 1.0
CG A:LYS642 4.9 12.0 1.0
C23 A:ZS3901 5.0 12.8 1.0

Fluorine binding site 3 out of 9 in 8s99

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Fluorine binding site 3 out of 9 in the Crystal Structure of the TYK2 Pseudokinase Domain in Complex with Compound 11


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 the TYK2 Pseudokinase Domain in Complex with Compound 11 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:19.8
occ:1.00
 F1 A:ZS3901 0.0 19.8 1.0
C2 A:ZS3901 1.3 21.1 1.0
C7 A:ZS3901 2.3 19.7 1.0
C3 A:ZS3901 2.3 22.1 1.0
N8 A:ZS3901 2.7 17.6 1.0
O33 A:ZS3901 2.8 16.8 1.0
CG2 A:VAL697 3.0 16.8 0.5
C32 A:ZS3901 3.0 16.5 1.0
NE A:ARG738 3.2 16.4 1.0
CZ A:ARG738 3.2 17.4 1.0
CG1 A:VAL697 3.4 17.8 0.5
N6 A:ZS3901 3.5 23.0 1.0
O A:HOH1051 3.5 36.4 1.0
C4 A:ZS3901 3.6 22.6 1.0
NH2 A:ARG738 3.6 18.2 1.0
CD A:ARG738 3.7 15.6 1.0
CG A:PRO694 3.7 13.8 1.0
C9 A:ZS3901 3.7 16.8 1.0
NH1 A:ARG738 3.7 17.9 1.0
CG2 A:VAL697 3.9 17.0 0.5
C5 A:ZS3901 4.0 23.1 1.0
CB A:PRO694 4.1 13.4 1.0
C12 A:ZS3901 4.1 15.4 1.0
CB A:VAL697 4.3 17.7 0.5
CB A:VAL697 4.3 16.9 0.5
O A:HOH1219 4.5 40.4 1.0
CD A:PRO694 4.5 13.9 1.0
OD1 A:ASP696 4.6 15.5 1.0
C10 A:ZS3901 4.7 16.5 1.0
N13 A:ZS3901 4.8 13.9 1.0
C11 A:ZS3901 4.9 15.7 1.0
CG1 A:VAL697 4.9 17.8 0.5

Fluorine binding site 4 out of 9 in 8s99

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Fluorine binding site 4 out of 9 in the Crystal Structure of the TYK2 Pseudokinase Domain in Complex with Compound 11


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 the TYK2 Pseudokinase Domain in Complex with Compound 11 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F901

b:18.4
occ:0.50
 F31 B:ZS3901 0.0 18.4 0.5
C30 B:ZS3901 1.4 16.8 0.5
C29 B:ZS3901 1.5 12.7 0.5
C29 B:ZS3901 2.5 16.6 0.5
C28 B:ZS3901 2.5 16.2 0.5
C28 B:ZS3901 2.5 12.7 0.5
N27 B:ZS3901 2.7 12.7 0.5
C30 B:ZS3901 2.8 12.6 0.5
N27 B:ZS3901 2.8 14.8 0.5
F31 B:ZS3901 3.2 13.3 0.5
C11 B:ZS3901 3.3 15.9 1.0
C10 B:ZS3901 3.3 16.7 1.0
O B:ARG738 3.4 13.3 1.0
CD B:ARG738 3.4 15.5 1.0
CG B:PRO694 3.6 13.2 1.0
CG B:ARG738 3.8 14.8 1.0
N24 B:ZS3901 3.8 13.4 1.0
C12 B:ZS3901 3.9 15.4 1.0
C9 B:ZS3901 4.0 16.9 1.0
C25 B:ZS3901 4.0 14.1 0.5
C25 B:ZS3901 4.0 13.0 0.5
CB B:PRO694 4.3 13.1 1.0
O B:HOH1016 4.3 21.1 1.0
C B:ARG738 4.4 13.6 1.0
C32 B:ZS3901 4.5 16.6 1.0
CD2 B:LEU741 4.5 13.4 1.0
N8 B:ZS3901 4.5 17.8 1.0
C23 B:ZS3901 4.6 13.1 1.0
N13 B:ZS3901 4.6 14.2 1.0
C14 B:ZS3901 4.6 13.6 1.0
C22 B:ZS3901 4.7 12.7 1.0
NE B:ARG738 4.7 16.2 1.0
OD1 B:ASN739 4.7 14.9 1.0
O26 B:ZS3901 4.7 13.3 0.5
O B:HOH1202 4.8 37.6 1.0
O26 B:ZS3901 4.9 12.5 0.5
CD B:PRO694 4.9 13.4 1.0

Fluorine binding site 5 out of 9 in 8s99

Go back to Fluorine Binding Sites List in 8s99
Fluorine binding site 5 out of 9 in the Crystal Structure of the TYK2 Pseudokinase Domain in Complex with Compound 11


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 the TYK2 Pseudokinase Domain in Complex with Compound 11 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F901

b:13.3
occ:0.50
 F31 B:ZS3901 0.0 13.3 0.5
C30 B:ZS3901 1.4 12.6 0.5
C28 B:ZS3901 1.7 16.2 0.5
C30 B:ZS3901 2.2 16.8 0.5
C28 B:ZS3901 2.5 12.7 0.5
C29 B:ZS3901 2.5 12.7 0.5
N27 B:ZS3901 2.7 14.8 0.5
C29 B:ZS3901 2.9 16.6 0.5
N27 B:ZS3901 3.0 12.7 0.5
F31 B:ZS3901 3.2 18.4 0.5
CG2 B:VAL603 3.3 14.1 1.0
C10 B:ZS3901 3.6 16.7 1.0
CE B:LYS642 3.7 13.3 1.0
NZ B:LYS642 3.7 13.8 1.0
C25 B:ZS3901 3.7 14.1 0.5
C25 B:ZS3901 3.8 13.0 0.5
C11 B:ZS3901 3.8 15.9 1.0
O B:HOH1113 4.0 21.9 1.0
O26 B:ZS3901 4.1 13.3 0.5
CG1 B:VAL603 4.1 13.4 1.0
O26 B:ZS3901 4.2 12.5 0.5
CB B:VAL603 4.2 13.7 1.0
CD B:LYS642 4.2 13.6 1.0
N24 B:ZS3901 4.7 13.4 1.0
O B:HOH1202 4.7 37.6 1.0
C9 B:ZS3901 4.7 16.9 1.0
CG B:LYS642 4.7 13.2 1.0
O B:HOH1187 4.8 27.0 1.0
C22 B:ZS3901 4.8 12.7 1.0
O B:HOH1016 4.9 21.1 1.0
O B:HOH1069 4.9 24.0 1.0

Fluorine binding site 6 out of 9 in 8s99

Go back to Fluorine Binding Sites List in 8s99
Fluorine binding site 6 out of 9 in the Crystal Structure of the TYK2 Pseudokinase Domain in Complex with Compound 11


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 the TYK2 Pseudokinase Domain in Complex with Compound 11 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F901

b:20.9
occ:1.00
 F1 B:ZS3901 0.0 20.9 1.0
C2 B:ZS3901 1.3 20.5 1.0
C7 B:ZS3901 2.4 19.6 1.0
C3 B:ZS3901 2.4 22.0 1.0
O33 B:ZS3901 2.8 15.7 1.0
N8 B:ZS3901 2.8 17.8 1.0
CG2 B:VAL697 2.9 16.3 0.5
C32 B:ZS3901 3.0 16.6 1.0
NE B:ARG738 3.2 16.2 1.0
CG1 B:VAL697 3.2 17.1 0.5
CZ B:ARG738 3.3 17.1 1.0
O B:HOH1093 3.4 28.1 1.0
NH2 B:ARG738 3.6 18.1 1.0
N6 B:ZS3901 3.6 22.0 1.0
C4 B:ZS3901 3.6 22.5 1.0
CG B:PRO694 3.7 13.2 1.0
NH1 B:ARG738 3.7 17.5 1.0
CD B:ARG738 3.8 15.5 1.0
C9 B:ZS3901 3.8 16.9 1.0
CG2 B:VAL697 3.9 16.8 0.5
CB B:PRO694 4.1 13.1 1.0
C5 B:ZS3901 4.1 22.9 1.0
C12 B:ZS3901 4.1 15.4 1.0
CB B:VAL697 4.2 17.3 0.5
CB B:VAL697 4.3 16.7 0.5
O B:HOH1224 4.5 37.3 1.0
CD B:PRO694 4.5 13.4 1.0
OD1 B:ASP696 4.6 14.9 1.0
N13 B:ZS3901 4.8 14.2 1.0
C10 B:ZS3901 4.8 16.7 1.0
CG1 B:VAL697 4.9 17.5 0.5
C11 B:ZS3901 4.9 15.9 1.0

Fluorine binding site 7 out of 9 in 8s99

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Fluorine binding site 7 out of 9 in the Crystal Structure of the TYK2 Pseudokinase Domain in Complex with Compound 11


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 the TYK2 Pseudokinase Domain in Complex with Compound 11 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F901

b:15.6
occ:0.50
 F31 C:ZS3901 0.0 15.6 0.5
C30 C:ZS3901 1.4 14.7 0.5
C29 C:ZS3901 1.7 12.6 0.5
C29 C:ZS3901 2.5 14.5 0.5
C28 C:ZS3901 2.5 14.3 0.5
C28 C:ZS3901 2.6 12.5 0.5
N27 C:ZS3901 2.6 12.6 0.5
N27 C:ZS3901 2.7 13.7 0.5
C30 C:ZS3901 2.9 12.5 0.5
C11 C:ZS3901 3.2 15.6 1.0
F31 C:ZS3901 3.2 13.2 0.5
C10 C:ZS3901 3.3 15.9 1.0
O C:ARG738 3.4 13.2 1.0
CG C:PRO694 3.4 12.9 1.0
CD C:ARG738 3.4 14.6 1.0
N24 C:ZS3901 3.6 12.8 1.0
C12 C:ZS3901 3.7 15.1 1.0
C25 C:ZS3901 3.9 13.3 0.5
CG C:ARG738 3.9 14.1 1.0
C25 C:ZS3901 3.9 12.7 0.5
C9 C:ZS3901 4.0 16.3 1.0
CB C:PRO694 4.2 12.7 1.0
C23 C:ZS3901 4.3 12.8 1.0
O C:HOH1073 4.3 23.6 1.0
C14 C:ZS3901 4.4 13.4 1.0
C32 C:ZS3901 4.4 15.9 1.0
CD2 C:LEU741 4.4 13.5 1.0
N13 C:ZS3901 4.4 14.3 1.0
C C:ARG738 4.4 13.1 1.0
N8 C:ZS3901 4.5 17.1 1.0
C22 C:ZS3901 4.5 12.6 1.0
CD C:PRO694 4.6 13.2 1.0
O26 C:ZS3901 4.7 12.8 0.5
NE C:ARG738 4.8 15.3 1.0
O26 C:ZS3901 4.8 12.4 0.5
OD1 C:ASN739 5.0 15.1 1.0

Fluorine binding site 8 out of 9 in 8s99

Go back to Fluorine Binding Sites List in 8s99
Fluorine binding site 8 out of 9 in the Crystal Structure of the TYK2 Pseudokinase Domain in Complex with Compound 11


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 the TYK2 Pseudokinase Domain in Complex with Compound 11 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F901

b:13.2
occ:0.50
 F31 C:ZS3901 0.0 13.2 0.5
C30 C:ZS3901 1.3 12.5 0.5
C28 C:ZS3901 1.6 14.3 0.5
C30 C:ZS3901 2.1 14.7 0.5
C28 C:ZS3901 2.4 12.5 0.5
C29 C:ZS3901 2.4 12.6 0.5
N27 C:ZS3901 2.6 13.7 0.5
C29 C:ZS3901 2.7 14.5 0.5
N27 C:ZS3901 2.9 12.6 0.5
CG2 C:VAL603 3.1 13.6 1.0
F31 C:ZS3901 3.2 15.6 0.5
C10 C:ZS3901 3.6 15.9 1.0
CE C:LYS642 3.6 13.6 1.0
C25 C:ZS3901 3.6 13.3 0.5
C25 C:ZS3901 3.7 12.7 0.5
NZ C:LYS642 3.7 14.0 1.0
C11 C:ZS3901 3.8 15.6 1.0
O C:HOH1117 3.9 24.6 1.0
O26 C:ZS3901 4.0 12.8 0.5
O26 C:ZS3901 4.0 12.4 0.5
CG1 C:VAL603 4.1 13.3 1.0
CB C:VAL603 4.1 13.4 1.0
CD C:LYS642 4.3 13.6 1.0
N24 C:ZS3901 4.6 12.8 1.0
C22 C:ZS3901 4.7 12.6 1.0
O C:HOH1175 4.7 25.9 1.0
C9 C:ZS3901 4.8 16.3 1.0
CG C:LYS642 4.8 13.1 1.0
O C:HOH1073 4.8 23.6 1.0
O C:HOH1036 5.0 19.3 1.0
C23 C:ZS3901 5.0 12.8 1.0

Fluorine binding site 9 out of 9 in 8s99

Go back to Fluorine Binding Sites List in 8s99
Fluorine binding site 9 out of 9 in the Crystal Structure of the TYK2 Pseudokinase Domain in Complex with Compound 11


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 the TYK2 Pseudokinase Domain in Complex with Compound 11 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F901

b:18.9
occ:1.00
 F1 C:ZS3901 0.0 18.9 1.0
C2 C:ZS3901 1.3 19.1 1.0
C7 C:ZS3901 2.4 18.9 1.0
C3 C:ZS3901 2.4 20.8 1.0
N8 C:ZS3901 2.8 17.1 1.0
O33 C:ZS3901 2.8 16.3 1.0
CG2 C:VAL697 2.9 15.7 0.5
C32 C:ZS3901 3.0 15.9 1.0
NE C:ARG738 3.2 15.3 1.0
CZ C:ARG738 3.2 16.0 1.0
CG1 C:VAL697 3.3 16.3 0.5
O C:HOH1093 3.5 26.7 1.0
NH2 C:ARG738 3.6 16.9 1.0
N6 C:ZS3901 3.6 20.9 1.0
C4 C:ZS3901 3.6 20.8 1.0
NH1 C:ARG738 3.7 16.4 1.0
CD C:ARG738 3.7 14.6 1.0
CG C:PRO694 3.8 12.9 1.0
C9 C:ZS3901 3.8 16.3 1.0
CG2 C:VAL697 4.0 15.8 0.5
C5 C:ZS3901 4.1 20.9 1.0
C12 C:ZS3901 4.2 15.1 1.0
CB C:PRO694 4.2 12.7 1.0
CB C:VAL697 4.2 16.3 0.5
CB C:VAL697 4.3 16.0 0.5
OD1 C:ASP696 4.5 14.9 1.0
CD C:PRO694 4.6 13.2 1.0
O C:HOH1227 4.6 32.9 1.0
C10 C:ZS3901 4.8 15.9 1.0
N13 C:ZS3901 4.9 14.3 1.0
CG1 C:VAL697 4.9 16.9 0.5
C11 C:ZS3901 4.9 15.6 1.0

Reference:

S.Leit, J.Greenwood, S.Carriero, S.Mondal, R.Abel, M.Ashwell, H.Blanchette, N.A.Boyles, M.Cartwright, A.Collis, S.Feng, P.Ghanakota, G.C.Harriman, V.Hosagrahara, N.Kaila, R.Kapeller, S.B.Rafi, D.L.Romero, P.M.Tarantino, J.Timaniya, A.V.Toms, R.T.Wester, W.Westlin, B.Srivastava, W.Miao, P.Tummino, J.J.Mcelwee, S.D.Edmondson, C.E.Masse. Discovery of A Potent and Selective Tyrosine Kinase 2 Inhibitor: Tak-279. J.Med.Chem. 2023.
ISSN: ISSN 0022-2623
PubMed: 37427891
DOI: 10.1021/ACS.JMEDCHEM.3C00600
Page generated: Thu Dec 28 04:44:31 2023

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