Fluorine in PDB 6bln: Btk Complex with Compound 13

All present enzymatic activity of Btk Complex with Compound 13:
2.7.10.2;

The structure of Btk Complex with Compound 13, PDB code: 6bln was solved by J.R.Kiefer, C.Eigenbrot, C.L.Yu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.07 / 1.30
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	107.823, 107.823, 41.866, 90.00, 90.00, 120.00
R / Rfree (%)	15.6 / 17.6

The binding sites of Fluorine atom in the Btk Complex with Compound 13 (pdb code 6bln). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Btk Complex with Compound 13, PDB code: 6bln:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Btk Complex with Compound 13


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Btk Complex with Compound 13 within 5.0Å range: probe atom residue distance (Å) B Occ A:F704 b:13.1 occ:1.00 F1 A:DY4704 0.0 13.1 1.0 C8 A:DY4704 1.3 10.8 1.0 C9 A:DY4704 2.3 11.9 1.0 C7 A:DY4704 2.4 11.6 1.0 N6 A:DY4704 2.7 13.6 1.0 N4 A:DY4704 2.7 12.1 1.0 C5 A:DY4704 2.9 11.2 1.0 O A:HOH809 3.2 17.5 1.0 O A:HOH919 3.3 22.3 1.0 O A:HOH886 3.4 28.4 1.0 HZ3 A:LYS430 3.4 32.2 1.0 HZ1 A:LYS430 3.4 32.2 1.0 OD2 A:ASP539 3.5 35.4 1.0 C19 A:DY4704 3.6 14.1 1.0 HD11 A:LEU528 3.6 13.5 1.0 C21 A:DY4704 3.6 12.2 1.0 C10 A:DY4704 3.7 17.5 1.0 NZ A:LYS430 3.7 26.8 1.0 HZ2 A:LYS430 3.7 32.2 1.0 HD21 A:LEU528 3.7 18.1 1.0 N5 A:DY4704 3.9 10.8 1.0 C4 A:DY4704 4.1 10.2 1.0 C20 A:DY4704 4.1 13.3 1.0 HG A:SER538 4.1 19.2 1.0 O2 A:DY4704 4.1 16.0 1.0 OG A:SER538 4.2 16.0 1.0 O A:HOH837 4.3 16.7 1.0 O A:HOH989 4.4 27.3 1.0 HG11 A:VAL416 4.4 17.3 1.0 CG A:ASP539 4.4 28.1 1.0 OD1 A:ASP539 4.4 24.6 1.0 HG21 A:VAL416 4.5 19.0 1.0 H21 A:DY4704 4.5 14.6 1.0 CD1 A:LEU528 4.5 11.2 1.0 H4 A:DY4704 4.7 12.3 1.0 CD2 A:LEU528 4.7 15.0 1.0 F2 A:DY4704 4.7 17.9 1.0 C11 A:DY4704 4.7 13.6 1.0 C6 A:DY4704 4.9 11.5 1.0 HG A:LEU528 4.9 11.3 1.0 HD13 A:LEU528 4.9 13.5 1.0 C3 A:DY4704 5.0 9.8 1.0

Fluorine binding site 2 out of 2 in the Btk Complex with Compound 13


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Btk Complex with Compound 13 within 5.0Å range: probe atom residue distance (Å) B Occ A:F704 b:17.9 occ:1.00 F2 A:DY4704 0.0 17.9 1.0 C19 A:DY4704 1.4 14.1 1.0 C9 A:DY4704 2.3 11.9 1.0 C20 A:DY4704 2.4 13.3 1.0 HA3 A:GLY411 2.4 21.6 1.0 H20 A:DY4704 2.6 15.9 1.0 N6 A:DY4704 2.8 13.6 1.0 O2 A:DY4704 2.9 16.0 1.0 CA A:GLY411 3.0 18.0 1.0 C10 A:DY4704 3.0 17.5 1.0 HA2 A:GLY411 3.1 21.6 1.0 N A:GLY411 3.2 16.8 1.0 O A:THR410 3.4 20.4 1.0 C A:THR410 3.4 17.7 1.0 HG21 A:VAL416 3.5 19.0 1.0 H A:GLY411 3.6 20.2 1.0 C8 A:DY4704 3.6 10.8 1.0 C21 A:DY4704 3.6 12.2 1.0 HG23 A:VAL416 3.9 19.0 1.0 C7 A:DY4704 4.1 11.6 1.0 O A:HOH950 4.1 26.6 1.0 CG2 A:VAL416 4.2 15.8 1.0 C11 A:DY4704 4.3 13.6 1.0 O A:HOH883 4.4 17.8 1.0 O A:HOH987 4.4 48.9 1.0 C A:GLY411 4.4 17.8 1.0 CA A:THR410 4.4 18.4 1.0 H A:GLN412 4.5 22.5 1.0 H21 A:DY4704 4.5 14.6 1.0 HA A:THR410 4.5 22.1 1.0 N A:THR410 4.6 19.3 1.0 H A:THR410 4.6 23.1 1.0 F1 A:DY4704 4.7 13.1 1.0 O A:HOH989 4.7 27.3 1.0 HB A:VAL416 4.8 18.1 1.0 HG22 A:VAL416 4.8 19.0 1.0 N A:GLN412 4.8 18.7 1.0

E.Nittinger, P.Gibbons, C.Eigenbrot, D.R.Davies, B.Maurer, C.L.Yu, J.R.Kiefer, A.Kuglstatter, J.Murray, D.F.Ortwine, Y.Tang, V.Tsui. Water Molecules in Protein-Ligand Interfaces. Evaluation of Software Tools and Sar Comparison. J. Comput. Aided Mol. Des. V. 33 307 2019.
ISSN: ISSN 1573-4951
PubMed: 30756207
DOI: 10.1007/S10822-019-00187-Y