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Fluorine in PDB 6x3p: Co-Structure of Btk Kinase Domain with L-005298385 Inhibitor

Enzymatic activity of Co-Structure of Btk Kinase Domain with L-005298385 Inhibitor

All present enzymatic activity of Co-Structure of Btk Kinase Domain with L-005298385 Inhibitor:
2.7.10.2;

Protein crystallography data

The structure of Co-Structure of Btk Kinase Domain with L-005298385 Inhibitor, PDB code: 6x3p was solved by T.O.Fischmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.33 / 1.34
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 72.010, 104.640, 38.000, 90.00, 90.00, 90.00
R / Rfree (%) 20.4 / 21.7

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Co-Structure of Btk Kinase Domain with L-005298385 Inhibitor (pdb code 6x3p). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Co-Structure of Btk Kinase Domain with L-005298385 Inhibitor, PDB code: 6x3p:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 6x3p

Go back to Fluorine Binding Sites List in 6x3p
Fluorine binding site 1 out of 6 in the Co-Structure of Btk Kinase Domain with L-005298385 Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Co-Structure of Btk Kinase Domain with L-005298385 Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F701

b:16.9
occ:1.00
F37 A:UM4701 0.0 16.9 1.0
C36 A:UM4701 1.3 15.4 1.0
F38 A:UM4701 2.1 15.6 1.0
F39 A:UM4701 2.1 14.8 1.0
C34 A:UM4701 2.3 9.7 1.0
C35 A:UM4701 2.8 10.4 1.0
CZ A:PHE442 3.3 17.8 1.0
C33 A:UM4701 3.5 10.4 1.0
CD1 A:ILE472 3.6 15.5 1.0
CE1 A:PHE442 3.6 19.2 1.0
CG1 A:ILE472 3.8 13.5 1.0
CB A:ALA446 3.9 11.5 1.0
CG2 A:ILE472 4.1 11.7 1.0
CE2 A:PHE442 4.1 21.6 1.0
CD2 A:LEU542 4.2 16.6 1.0
C30 A:UM4701 4.2 10.3 1.0
CD1 A:LEU542 4.2 14.3 1.0
CD1 A:PHE442 4.6 18.6 1.0
CB A:ILE472 4.6 11.1 1.0
O28 A:UM4701 4.6 10.6 1.0
CA A:ALA446 4.6 10.0 1.0
C32 A:UM4701 4.6 9.6 1.0
CG A:LEU542 4.8 13.7 1.0
N31 A:UM4701 4.9 10.3 1.0

Fluorine binding site 2 out of 6 in 6x3p

Go back to Fluorine Binding Sites List in 6x3p
Fluorine binding site 2 out of 6 in the Co-Structure of Btk Kinase Domain with L-005298385 Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Co-Structure of Btk Kinase Domain with L-005298385 Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F701

b:15.6
occ:1.00
F38 A:UM4701 0.0 15.6 1.0
C36 A:UM4701 1.3 15.4 1.0
F37 A:UM4701 2.1 16.9 1.0
F39 A:UM4701 2.1 14.8 1.0
C34 A:UM4701 2.3 9.7 1.0
C35 A:UM4701 3.0 10.4 1.0
C33 A:UM4701 3.3 10.4 1.0
CG2 A:ILE472 3.5 11.7 1.0
CD1 A:LEU460 3.5 12.9 1.0
CB A:ALA446 3.6 11.5 1.0
CD2 A:LEU460 3.8 11.0 1.0
CA A:ALA446 4.0 10.0 1.0
CD1 A:ILE472 4.2 15.5 1.0
CG A:LEU460 4.2 10.1 1.0
CE A:MET450 4.2 10.9 1.0
C30 A:UM4701 4.3 10.3 1.0
C32 A:UM4701 4.5 9.6 1.0
CG1 A:ILE472 4.5 13.5 1.0
O A:ALA446 4.6 11.6 1.0
CB A:ILE472 4.7 11.1 1.0
C A:ALA446 4.7 11.8 1.0
CB A:LEU460 4.8 8.4 1.0
CG1 A:VAL463 4.8 14.7 1.0
N31 A:UM4701 4.9 10.3 1.0

Fluorine binding site 3 out of 6 in 6x3p

Go back to Fluorine Binding Sites List in 6x3p
Fluorine binding site 3 out of 6 in the Co-Structure of Btk Kinase Domain with L-005298385 Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Co-Structure of Btk Kinase Domain with L-005298385 Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F701

b:14.8
occ:1.00
F39 A:UM4701 0.0 14.8 1.0
C36 A:UM4701 1.3 15.4 1.0
F37 A:UM4701 2.1 16.9 1.0
F38 A:UM4701 2.1 15.6 1.0
C34 A:UM4701 2.3 9.7 1.0
C33 A:UM4701 2.7 10.4 1.0
CA A:ALA446 3.3 10.0 1.0
CB A:ALA446 3.3 11.5 1.0
C35 A:UM4701 3.6 10.4 1.0
CD2 A:LEU542 3.6 16.6 1.0
SD A:MET449 4.0 12.2 1.0
N A:ALA446 4.1 10.4 1.0
C32 A:UM4701 4.1 9.6 1.0
CD1 A:LEU460 4.3 12.9 1.0
C A:ALA446 4.5 11.8 1.0
O A:ALA446 4.6 11.6 1.0
CE1 A:PHE442 4.7 19.2 1.0
CD1 A:LEU542 4.7 14.3 1.0
CB A:MET449 4.7 9.9 1.0
C30 A:UM4701 4.7 10.3 1.0
CG A:LEU542 4.7 13.7 1.0
C A:GLU445 4.8 11.5 1.0
CZ A:PHE442 4.8 17.8 1.0
O A:PHE442 4.9 12.0 1.0
O A:GLU445 4.9 11.1 1.0
N31 A:UM4701 4.9 10.3 1.0

Fluorine binding site 4 out of 6 in 6x3p

Go back to Fluorine Binding Sites List in 6x3p
Fluorine binding site 4 out of 6 in the Co-Structure of Btk Kinase Domain with L-005298385 Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Co-Structure of Btk Kinase Domain with L-005298385 Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F702

b:14.6
occ:1.00
F37 A:UM4702 0.0 14.6 1.0
C36 A:UM4702 1.3 15.7 1.0
F39 A:UM4702 2.1 15.8 1.0
F38 A:UM4702 2.1 16.2 1.0
C34 A:UM4702 2.3 11.8 1.0
C35 A:UM4702 2.7 11.0 1.0
CE2 A:TYR461 3.3 9.9 1.0
CD2 A:TYR461 3.4 9.1 1.0
O A:HOH982 3.5 36.3 1.0
C33 A:UM4702 3.6 12.1 1.0
CG1 A:VAL427 3.7 9.9 1.0
CZ A:TYR461 3.8 10.8 1.0
O A:HOH955 3.8 27.6 1.0
CB A:TYR425 3.9 11.9 1.0
CG A:TYR461 4.0 8.5 1.0
C30 A:UM4702 4.1 10.0 1.0
CE1 A:TYR461 4.3 10.5 1.0
O A:ASP426 4.3 11.3 1.0
OH A:TYR461 4.3 13.2 1.0
CD1 A:TYR461 4.4 8.9 1.0
O28 A:UM4702 4.4 12.7 1.0
CG A:TYR425 4.5 15.7 1.0
CD1 A:TYR425 4.6 19.0 1.0
C32 A:UM4702 4.7 13.6 1.0
CB A:TYR461 4.8 9.7 1.0
N31 A:UM4702 4.9 12.4 1.0
CE3 A:TRP421 5.0 11.3 1.0

Fluorine binding site 5 out of 6 in 6x3p

Go back to Fluorine Binding Sites List in 6x3p
Fluorine binding site 5 out of 6 in the Co-Structure of Btk Kinase Domain with L-005298385 Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Co-Structure of Btk Kinase Domain with L-005298385 Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F702

b:16.2
occ:1.00
F38 A:UM4702 0.0 16.2 1.0
C36 A:UM4702 1.3 15.7 1.0
F37 A:UM4702 2.1 14.6 1.0
F39 A:UM4702 2.1 15.8 1.0
C34 A:UM4702 2.3 11.8 1.0
C35 A:UM4702 3.1 11.0 1.0
CG A:TYR425 3.1 15.7 1.0
CB A:TYR425 3.2 11.9 1.0
C33 A:UM4702 3.2 12.1 1.0
CE3 A:TRP421 3.3 11.3 1.0
CD1 A:TYR425 3.4 19.0 1.0
CZ3 A:TRP421 3.8 13.0 1.0
CD2 A:TYR425 3.8 16.4 1.0
CD2 A:TRP421 4.1 9.4 1.0
CE1 A:TYR425 4.2 20.9 1.0
O A:HOH982 4.2 36.3 1.0
C30 A:UM4702 4.3 10.0 1.0
C32 A:UM4702 4.3 13.6 1.0
CB A:TRP421 4.5 9.2 1.0
CE2 A:TYR425 4.6 17.8 1.0
CG A:TRP421 4.6 9.1 1.0
O A:HOH955 4.6 27.6 1.0
CA A:TYR425 4.7 10.1 1.0
CZ A:TYR425 4.7 23.7 1.0
CH2 A:TRP421 4.8 13.5 1.0
N31 A:UM4702 4.9 12.4 1.0
CG1 A:VAL427 4.9 9.9 1.0
CE2 A:TRP421 5.0 12.0 1.0

Fluorine binding site 6 out of 6 in 6x3p

Go back to Fluorine Binding Sites List in 6x3p
Fluorine binding site 6 out of 6 in the Co-Structure of Btk Kinase Domain with L-005298385 Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Co-Structure of Btk Kinase Domain with L-005298385 Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F702

b:15.8
occ:1.00
F39 A:UM4702 0.0 15.8 1.0
C36 A:UM4702 1.3 15.7 1.0
F37 A:UM4702 2.1 14.6 1.0
F38 A:UM4702 2.1 16.2 1.0
C34 A:UM4702 2.3 11.8 1.0
C33 A:UM4702 2.8 12.1 1.0
CB A:TRP421 3.1 9.2 1.0
CG1 A:VAL427 3.2 9.9 1.0
CG A:TRP421 3.4 9.1 1.0
CE3 A:TRP421 3.4 11.3 1.0
CD2 A:TRP421 3.5 9.4 1.0
C35 A:UM4702 3.6 11.0 1.0
CB A:TYR425 3.8 11.9 1.0
C32 A:UM4702 4.2 13.6 1.0
CD1 A:TRP421 4.2 11.6 1.0
CD2 A:TYR461 4.3 9.1 1.0
CE2 A:TRP421 4.4 12.0 1.0
CZ3 A:TRP421 4.4 13.0 1.0
CG A:TYR425 4.5 15.7 1.0
CA A:TRP421 4.5 9.4 1.0
O A:TYR425 4.6 10.9 1.0
CE2 A:TYR461 4.7 9.9 1.0
C30 A:UM4702 4.7 10.0 1.0
CB A:VAL427 4.7 10.6 1.0
NE1 A:TRP421 4.8 12.1 1.0
CG A:TYR461 4.9 8.5 1.0
N A:TRP421 4.9 9.0 1.0
N31 A:UM4702 5.0 12.4 1.0

Reference:

J.Liu, D.Guiadeen, A.Krikorian, X.Gao, J.Wang, S.Babu Boga, A.B.Alhassan, W.Yu, O.Selyutin, Y.Yu, R.Anand, J.Xu, J.Kelly, J.L.Duffy, S.Liu, C.Yang, H.Wu, J.Cai, C.Bennett, K.M.Maloney, S.Tyagarajan, Y.D.Gao, T.O.Fischmann, J.Presland, M.Mansueto, Z.Xu, E.Leccese, J.Zhang-Hoover, I.Knemeyer, C.G.Garlisi, P.Stivers, P.E.Brandish, A.Hicks, R.Kim, J.A.Kozlowski. Potent, Non-Covalent Reversible Btk Inhibitors with 8-Amino-Imidazo[1,5-A]Pyrazine Core Featuring 3-Position Bicyclic Ring Substitutes. Bioorg.Med.Chem.Lett. V. 30 27390 2020.
ISSN: ESSN 1464-3405
PubMed: 32738973
DOI: 10.1016/J.BMCL.2020.127390
Page generated: Tue Jul 15 17:19:56 2025

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