Fluorine in PDB 6bkw: Btk Complex with Compound 12

All present enzymatic activity of Btk Complex with Compound 12:
2.7.10.2;

The structure of Btk Complex with Compound 12, PDB code: 6bkw 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)	31.29 / 1.50
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	108.765, 108.765, 41.863, 90.00, 90.00, 120.00
R / Rfree (%)	16.3 / 19

The binding sites of Fluorine atom in the Btk Complex with Compound 12 (pdb code 6bkw). 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 12, PDB code: 6bkw:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Btk Complex with Compound 12


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 12 within 5.0Å range: probe atom residue distance (Å) B Occ A:F704 b:16.6 occ:1.00 F1 A:DXM704 0.0 16.6 1.0 C9 A:DXM704 1.3 13.3 1.0 C10 A:DXM704 2.3 14.4 1.0 C8 A:DXM704 2.4 12.3 1.0 N6 A:DXM704 2.7 15.9 1.0 N4 A:DXM704 2.7 14.5 1.0 C5 A:DXM704 2.9 12.6 1.0 O A:HOH806 3.1 22.3 1.0 O A:HOH865 3.3 30.6 1.0 HZ1 A:LYS430 3.3 28.4 1.0 OD2 A:ASP539 3.3 30.5 1.0 O A:HOH843 3.4 28.6 1.0 C20 A:DXM704 3.6 16.6 1.0 HZ3 A:LYS430 3.6 28.4 1.0 HD11 A:LEU528 3.6 19.1 1.0 C11 A:DXM704 3.6 18.1 1.0 C22 A:DXM704 3.6 13.7 1.0 NZ A:LYS430 3.8 23.6 1.0 HD21 A:LEU528 3.8 27.1 1.0 HZ2 A:LYS430 3.8 28.4 1.0 N5 A:DXM704 3.9 13.4 1.0 H63 A:DXM704 4.0 20.2 1.0 O2 A:DXM704 4.0 16.9 1.0 C21 A:DXM704 4.1 13.7 1.0 C4 A:DXM704 4.1 10.4 1.0 O A:HOH971 4.2 24.4 1.0 HG A:SER538 4.3 21.0 0.5 CG A:ASP539 4.3 27.2 1.0 HG21 A:VAL416 4.4 22.1 1.0 C6 A:DXM704 4.4 16.8 1.0 OG A:SER538 4.4 17.5 0.5 HG11 A:VAL416 4.5 20.6 1.0 OD1 A:ASP539 4.5 29.8 1.0 H22 A:DXM704 4.5 16.4 1.0 CD1 A:LEU528 4.5 15.9 1.0 C12 A:DXM704 4.6 15.5 1.0 OG A:SER538 4.7 20.4 0.5 F2 A:DXM704 4.7 20.6 1.0 H62 A:DXM704 4.7 20.2 1.0 O A:HOH914 4.7 26.3 1.0 CD2 A:LEU528 4.7 22.5 1.0 C7 A:DXM704 4.9 14.3 1.0 HB2 A:SER538 4.9 19.0 0.5 HD13 A:LEU528 4.9 19.1 1.0 C3 A:DXM704 5.0 12.2 1.0 C13 A:DXM704 5.0 12.6 1.0

Fluorine binding site 2 out of 2 in the Btk Complex with Compound 12


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 12 within 5.0Å range: probe atom residue distance (Å) B Occ A:F704 b:20.6 occ:1.00 F2 A:DXM704 0.0 20.6 1.0 C20 A:DXM704 1.4 16.6 1.0 C21 A:DXM704 2.4 13.7 1.0 C10 A:DXM704 2.4 14.4 1.0 HA3 A:GLY411 2.4 24.9 1.0 H21 A:DXM704 2.6 16.4 1.0 N6 A:DXM704 2.8 15.9 1.0 CA A:GLY411 3.0 20.7 1.0 O2 A:DXM704 3.0 16.9 1.0 N A:GLY411 3.1 20.0 1.0 HA2 A:GLY411 3.1 24.9 1.0 C11 A:DXM704 3.1 18.1 1.0 C A:THR410 3.3 19.6 1.0 O A:THR410 3.4 23.2 1.0 H A:GLY411 3.5 24.0 1.0 HG21 A:VAL416 3.5 22.1 1.0 C9 A:DXM704 3.6 13.3 1.0 C22 A:DXM704 3.6 13.7 1.0 HG23 A:VAL416 3.8 22.1 1.0 C8 A:DXM704 4.1 12.3 1.0 CG2 A:VAL416 4.1 18.4 1.0 O A:HOH944 4.2 28.8 1.0 O A:HOH896 4.3 19.6 1.0 CA A:THR410 4.3 16.9 1.0 HA A:THR410 4.3 20.3 1.0 C12 A:DXM704 4.3 15.5 1.0 C A:GLY411 4.4 17.9 1.0 N A:THR410 4.5 17.9 1.0 H A:GLN412 4.5 21.2 1.0 H22 A:DXM704 4.5 16.4 1.0 H A:THR410 4.6 21.6 1.0 F1 A:DXM704 4.7 16.6 1.0 HB A:VAL416 4.8 20.3 1.0 HG22 A:VAL416 4.8 22.1 1.0 N A:GLN412 4.8 17.7 1.0 O A:HOH971 4.9 24.4 1.0 O A:GLY414 4.9 19.6 1.0 C A:GLY409 4.9 19.9 1.0 O A:HOH951 5.0 39.3 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