Fluorine in PDB 5mxx: Crystal Structure of Human Sr Protein Kinase 1 (SRPK1) in Complex with Compound 1

The structure of Crystal Structure of Human Sr Protein Kinase 1 (SRPK1) in Complex with Compound 1, PDB code: 5mxx was solved by C.Tallant, C.Redondo, J.Batson, H.D.Toop, R.Babaebi-Jadidib, P.Savitsky, J.M.Elkins, J.A.Newman, N.Burgess-Brown, F.Von Delft, C.H.Arrowsmith, A.M.Edwards, C.Bountra, D.O.Bates, J.C.Morris, S.Knapp, Structuralgenomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.29 / 1.75
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	82.572, 82.572, 133.837, 90.00, 90.00, 90.00
R / Rfree (%)	17.3 / 20.5

The structure of Crystal Structure of Human Sr Protein Kinase 1 (SRPK1) in Complex with Compound 1 also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Fluorine atom in the Crystal Structure of Human Sr Protein Kinase 1 (SRPK1) in Complex with Compound 1 (pdb code 5mxx). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of Human Sr Protein Kinase 1 (SRPK1) in Complex with Compound 1, PDB code: 5mxx:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of Human Sr Protein Kinase 1 (SRPK1) in Complex with Compound 1


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 Human Sr Protein Kinase 1 (SRPK1) in Complex with Compound 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:F701 b:33.0 occ:1.00 F2 A:W4A701 0.0 33.0 1.0 C13 A:W4A701 1.3 32.1 1.0 F1 A:W4A701 2.1 34.5 1.0 F A:W4A701 2.1 35.7 1.0 C12 A:W4A701 2.3 27.4 1.0 C11 A:W4A701 2.8 23.3 1.0 C10 A:W4A701 3.6 25.8 1.0 CG1 A:VAL167 3.7 33.2 1.0 CG2 A:VAL223 3.8 30.1 1.0 CA A:GLY169 4.1 23.9 1.0 C2 A:W4A701 4.2 22.8 1.0 CD1 A:LEU231 4.2 34.7 1.0 CD2 A:LEU86 4.2 31.5 1.0 CE2 A:TYR227 4.4 34.3 1.0 N A:GLY169 4.5 23.6 1.0 O A:LEU168 4.6 27.2 1.0 O A:W4A701 4.6 25.3 1.0 CG1 A:ILE228 4.7 29.8 1.0 C9 A:W4A701 4.7 25.7 1.0 CD2 A:TYR227 4.7 33.4 1.0 C A:GLY169 4.8 22.2 1.0 C A:LEU168 4.8 28.1 1.0 CG1 A:VAL223 4.8 30.7 1.0 C3 A:W4A701 4.9 23.9 1.0 CB A:VAL223 4.9 30.9 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of Human Sr Protein Kinase 1 (SRPK1) in Complex with Compound 1


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 Human Sr Protein Kinase 1 (SRPK1) in Complex with Compound 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:F701 b:34.5 occ:1.00 F1 A:W4A701 0.0 34.5 1.0 C13 A:W4A701 1.3 32.1 1.0 F A:W4A701 2.0 35.7 1.0 F2 A:W4A701 2.1 33.0 1.0 C12 A:W4A701 2.4 27.4 1.0 C10 A:W4A701 3.0 25.8 1.0 C11 A:W4A701 3.4 23.3 1.0 NE2 A:HIS170 3.4 29.3 1.0 CA A:GLY169 3.5 23.9 1.0 CE2 A:TYR227 3.5 34.3 1.0 CG1 A:VAL223 3.5 30.7 1.0 CD2 A:HIS170 3.5 30.9 1.0 CG2 A:VAL223 3.7 30.1 1.0 N A:HIS170 3.8 22.4 1.0 C A:GLY169 3.9 22.2 1.0 CE1 A:HIS170 3.9 28.8 1.0 CG A:HIS170 4.1 25.9 1.0 ND1 A:HIS170 4.2 28.4 1.0 CD2 A:TYR227 4.2 33.4 1.0 CB A:VAL223 4.3 30.9 1.0 C9 A:W4A701 4.3 25.7 1.0 CZ A:TYR227 4.4 34.9 1.0 OH A:TYR227 4.4 38.0 1.0 N A:GLY169 4.5 23.6 1.0 C2 A:W4A701 4.6 22.8 1.0 CA A:HIS170 4.7 21.8 1.0 O A:GLY169 4.7 22.3 1.0 CD1 A:LEU231 4.8 34.7 1.0 O A:LEU168 4.9 27.2 1.0 C3 A:W4A701 4.9 23.9 1.0 CB A:HIS170 4.9 23.1 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of Human Sr Protein Kinase 1 (SRPK1) in Complex with Compound 1


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 Human Sr Protein Kinase 1 (SRPK1) in Complex with Compound 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:F701 b:35.7 occ:1.00 F A:W4A701 0.0 35.7 1.0 C13 A:W4A701 1.3 32.1 1.0 F1 A:W4A701 2.0 34.5 1.0 F2 A:W4A701 2.1 33.0 1.0 C12 A:W4A701 2.3 27.4 1.0 C10 A:W4A701 2.8 25.8 1.0 CD1 A:LEU231 3.2 34.7 1.0 C11 A:W4A701 3.5 23.3 1.0 CE2 A:TYR227 3.6 34.3 1.0 CD2 A:LEU86 3.7 31.5 1.0 NE2 A:HIS170 4.1 29.3 1.0 CE1 A:HIS170 4.1 28.8 1.0 C9 A:W4A701 4.1 25.7 1.0 OH A:TYR227 4.2 38.0 1.0 CZ A:TYR227 4.4 34.9 1.0 CD2 A:TYR227 4.5 33.4 1.0 CG A:LEU231 4.6 33.8 1.0 C2 A:W4A701 4.7 22.8 1.0 ND1 A:HIS170 4.7 28.4 1.0 CD2 A:HIS170 4.7 30.9 1.0 C3 A:W4A701 4.9 23.9 1.0

J.Batson, H.D.Toop, C.Redondo, R.Babaei-Jadidi, A.Chaikuad, S.F.Wearmouth, B.Gibbons, C.Allen, C.Tallant, J.Zhang, C.Du, J.C.Hancox, T.Hawtrey, J.Da Rocha, R.Griffith, S.Knapp, D.O.Bates, J.C.Morris. Development of Potent, Selective SRPK1 Inhibitors As Potential Topical Therapeutics For Neovascular Eye Disease. Acs Chem. Biol. V. 12 825 2017.
ISSN: ESSN 1554-8937
PubMed: 28135068
DOI: 10.1021/ACSCHEMBIO.6B01048