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Fluorine in PDB 6w8i: Ternary Complex Structure - Btk Ciap Compound 15

Enzymatic activity of Ternary Complex Structure - Btk Ciap Compound 15

All present enzymatic activity of Ternary Complex Structure - Btk Ciap Compound 15:
2.3.2.27; 2.7.10.2;

Protein crystallography data

The structure of Ternary Complex Structure - Btk Ciap Compound 15, PDB code: 6w8i was solved by M.F.Calabrese, J.S.Schiemer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.74 / 3.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 69.250, 109.490, 188.740, 90.00, 90.00, 90.00
R / Rfree (%) 21.1 / 25.1

Other elements in 6w8i:

The structure of Ternary Complex Structure - Btk Ciap Compound 15 also contains other interesting chemical elements:

Zinc (Zn) 3 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Ternary Complex Structure - Btk Ciap Compound 15 (pdb code 6w8i). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Ternary Complex Structure - Btk Ciap Compound 15, PDB code: 6w8i:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 6w8i

Go back to Fluorine Binding Sites List in 6w8i
Fluorine binding site 1 out of 6 in the Ternary Complex Structure - Btk Ciap Compound 15


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Ternary Complex Structure - Btk Ciap Compound 15 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F701

b:59.3
occ:1.00
 F74 C:TKY701 0.0 59.3 1.0
C73 C:TKY701 1.4 57.3 1.0
C72 C:TKY701 2.3 55.8 1.0
C68 C:TKY701 2.3 56.8 1.0
O67 C:TKY701 2.7 56.8 1.0
CG2 C:ILE472 3.4 58.3 1.0
CD C:LYS430 3.5 54.9 1.0
C71 C:TKY701 3.6 55.7 1.0
C69 C:TKY701 3.6 56.6 1.0
C64 C:TKY701 3.6 56.8 1.0
CD2 C:LEU542 3.7 52.2 1.0
CB C:ILE472 3.7 58.4 1.0
CG1 C:ILE472 3.8 59.4 1.0
OD1 C:ASP539 3.9 67.7 1.0
C70 C:TKY701 4.1 57.3 1.0
C63 C:TKY701 4.2 57.3 1.0
CE C:LYS430 4.3 54.9 1.0
CD1 C:ILE432 4.3 68.8 1.0
CD1 C:LEU542 4.3 51.3 1.0
CG C:LYS430 4.6 53.6 1.0
CB C:LYS430 4.6 48.5 1.0
C65 C:TKY701 4.6 55.8 1.0
CG C:LEU542 4.6 50.5 1.0
F75 C:TKY701 4.7 53.9 1.0
CD1 C:ILE472 4.8 68.8 1.0

Fluorine binding site 2 out of 6 in 6w8i

Go back to Fluorine Binding Sites List in 6w8i
Fluorine binding site 2 out of 6 in the Ternary Complex Structure - Btk Ciap Compound 15


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Ternary Complex Structure - Btk Ciap Compound 15 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F701

b:53.9
occ:1.00
 F75 C:TKY701 0.0 53.9 1.0
C71 C:TKY701 1.4 55.7 1.0
C72 C:TKY701 2.3 55.8 1.0
C70 C:TKY701 2.3 57.3 1.0
N C:PHE540 3.1 40.0 1.0
O C:PHE540 3.3 43.0 1.0
CG C:PHE540 3.4 43.1 1.0
CD1 C:PHE540 3.5 45.2 1.0
CD2 C:PHE540 3.5 45.0 1.0
C C:ASP539 3.5 44.7 1.0
SD C:MET449 3.6 58.8 1.0
C73 C:TKY701 3.6 57.3 1.0
CA C:ASP539 3.6 41.4 1.0
C69 C:TKY701 3.6 56.6 1.0
CE2 C:PHE540 3.6 47.4 1.0
CE1 C:PHE540 3.6 45.5 1.0
CZ C:PHE540 3.7 44.8 1.0
N C:ASP539 3.7 41.1 1.0
CA C:PHE540 3.8 39.6 1.0
C C:PHE540 3.9 43.4 1.0
C68 C:TKY701 4.1 56.8 1.0
CB C:PHE540 4.2 41.4 1.0
CD1 C:LEU460 4.3 49.4 1.0
O C:ASP539 4.5 44.9 1.0
C C:SER538 4.6 43.2 1.0
F74 C:TKY701 4.7 59.3 1.0
CG C:MET449 4.7 56.2 1.0
CB C:LEU542 4.9 46.0 1.0

Fluorine binding site 3 out of 6 in 6w8i

Go back to Fluorine Binding Sites List in 6w8i
Fluorine binding site 3 out of 6 in the Ternary Complex Structure - Btk Ciap Compound 15


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Ternary Complex Structure - Btk Ciap Compound 15 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F502

b:76.9
occ:1.00
 F74 D:TKY502 0.0 76.9 1.0
C73 D:TKY502 1.4 73.9 1.0
C72 D:TKY502 2.3 75.9 1.0
C68 D:TKY502 2.3 66.7 1.0
O67 D:TKY502 2.7 60.6 1.0
CD A:LYS430 3.3 59.2 1.0
C71 D:TKY502 3.6 75.0 1.0
C64 D:TKY502 3.6 54.4 1.0
C69 D:TKY502 3.6 67.9 1.0
CG2 A:ILE472 3.8 40.4 1.0
CE A:LYS430 3.9 62.9 1.0
CG A:LYS430 4.0 53.3 1.0
C70 D:TKY502 4.1 71.8 1.0
C63 D:TKY502 4.1 49.2 1.0
CB A:LYS430 4.2 50.9 1.0
CB A:ILE472 4.3 40.4 1.0
C65 D:TKY502 4.5 52.1 1.0
CG1 A:ILE472 4.5 40.8 1.0
CD2 A:LEU542 4.6 81.8 1.0
OD1 A:ASP539 4.7 69.6 1.0
F75 D:TKY502 4.7 74.7 1.0

Fluorine binding site 4 out of 6 in 6w8i

Go back to Fluorine Binding Sites List in 6w8i
Fluorine binding site 4 out of 6 in the Ternary Complex Structure - Btk Ciap Compound 15


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Ternary Complex Structure - Btk Ciap Compound 15 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F502

b:74.7
occ:1.00
 F75 D:TKY502 0.0 74.7 1.0
C71 D:TKY502 1.4 75.0 1.0
C72 D:TKY502 2.3 75.9 1.0
C70 D:TKY502 2.3 71.8 1.0
CD1 A:LEU542 3.3 82.2 1.0
N A:PHE540 3.4 66.8 1.0
CA A:ASP539 3.4 62.7 1.0
N A:ASP539 3.4 61.5 1.0
C73 D:TKY502 3.6 73.9 1.0
C69 D:TKY502 3.6 67.9 1.0
O A:PHE540 3.7 72.7 1.0
CD1 A:PHE540 3.7 73.7 1.0
C A:ASP539 3.7 69.5 1.0
CE1 A:PHE540 3.8 74.7 1.0
C68 D:TKY502 4.1 66.7 1.0
CG A:PHE540 4.2 70.0 1.0
CD2 A:LEU542 4.3 81.8 1.0
CZ A:PHE540 4.3 73.9 1.0
CA A:PHE540 4.4 66.9 1.0
CG A:LEU542 4.4 81.8 1.0
C A:PHE540 4.4 73.4 1.0
C A:SER538 4.5 61.1 1.0
CD2 A:PHE540 4.7 72.2 1.0
F74 D:TKY502 4.7 76.9 1.0
CE2 A:PHE540 4.7 75.6 1.0
O A:ASP539 4.7 70.0 1.0
CB A:ASP539 4.8 64.5 1.0
CB A:PHE540 4.9 68.3 1.0

Fluorine binding site 5 out of 6 in 6w8i

Go back to Fluorine Binding Sites List in 6w8i
Fluorine binding site 5 out of 6 in the Ternary Complex Structure - Btk Ciap Compound 15


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Ternary Complex Structure - Btk Ciap Compound 15 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F502

b:54.3
occ:1.00
 F74 E:TKY502 0.0 54.3 1.0
C73 E:TKY502 1.4 48.9 1.0
C72 E:TKY502 2.3 47.4 1.0
C68 E:TKY502 2.3 44.8 1.0
O67 E:TKY502 2.7 42.8 1.0
CD B:LYS430 3.3 46.9 1.0
NZ B:LYS430 3.4 37.7 1.0
C64 E:TKY502 3.5 40.6 1.0
C71 E:TKY502 3.6 46.8 1.0
C69 E:TKY502 3.6 45.0 1.0
CE B:LYS430 3.8 40.8 1.0
C63 E:TKY502 4.0 42.2 1.0
CG2 B:ILE472 4.1 43.3 1.0
C70 E:TKY502 4.1 46.7 1.0
OD2 B:ASP539 4.1 52.2 1.0
CG B:LEU542 4.4 33.8 1.0
CD1 B:LEU542 4.5 33.8 1.0
CG B:ASP539 4.5 51.5 1.0
C65 E:TKY502 4.5 38.6 1.0
CG B:LYS430 4.5 45.6 1.0
CB B:ILE472 4.6 43.6 1.0
CG1 B:ILE472 4.6 45.2 1.0
OD1 B:ASP539 4.7 57.9 1.0
F75 E:TKY502 4.7 45.9 1.0
CB B:LYS430 4.8 42.7 1.0
CB B:LEU542 4.9 33.9 1.0

Fluorine binding site 6 out of 6 in 6w8i

Go back to Fluorine Binding Sites List in 6w8i
Fluorine binding site 6 out of 6 in the Ternary Complex Structure - Btk Ciap Compound 15


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Ternary Complex Structure - Btk Ciap Compound 15 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F502

b:45.9
occ:1.00
 F75 E:TKY502 0.0 45.9 1.0
C71 E:TKY502 1.4 46.8 1.0
C72 E:TKY502 2.3 47.4 1.0
C70 E:TKY502 2.4 46.7 1.0
O B:PHE540 3.0 19.2 1.0
N B:PHE540 3.3 35.2 1.0
CA B:ASP539 3.5 37.3 1.0
C73 E:TKY502 3.6 48.9 1.0
C B:ASP539 3.6 40.9 1.0
SD B:MET449 3.6 50.0 1.0
C69 E:TKY502 3.6 45.0 1.0
N B:ASP539 3.7 36.8 1.0
CD2 B:PHE540 3.8 47.6 1.0
C B:PHE540 3.8 40.4 1.0
CE2 B:PHE540 3.9 47.9 1.0
CG B:PHE540 3.9 44.9 1.0
CB B:LEU542 4.1 33.9 1.0
CA B:PHE540 4.1 40.1 1.0
CZ B:PHE540 4.1 47.2 1.0
C68 E:TKY502 4.1 44.8 1.0
CD1 B:PHE540 4.1 47.6 1.0
CE1 B:PHE540 4.2 49.7 1.0
CG B:MET449 4.2 44.8 1.0
O B:ASP539 4.4 40.7 1.0
N B:LEU542 4.6 33.3 1.0
CB B:PHE540 4.6 42.1 1.0
CD1 B:LEU460 4.6 49.3 1.0
CG B:LEU542 4.6 33.8 1.0
F74 E:TKY502 4.7 54.3 1.0
C B:SER538 4.7 39.3 1.0
CE B:MET449 4.9 46.9 1.0
CB B:ASP539 4.9 39.1 1.0
CA B:LEU542 5.0 33.8 1.0

Reference:

M.F.Calabrese, J.S.Schiemer, R.Horst, Y.Meng, J.Montgomery, Y.Xu, X.Feng, K.Borzilleri, D.P.Uccello, C.Leverett, S.Brown, Y.Che, M.F.Brown, M.M.Hayward, A.M.Gilbert, M.C.Noe. Structural Characterization of Btk:Protac:Ciap Ternary Complexes: From Snapshots to Ensembles Nat.Chem.Biol. 2020.
ISSN: ESSN 1552-4469
Page generated: Fri Aug 2 03:38:39 2024

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