Fluorine in PDB 5my8: Crystal Structure of SRPK1 in Complex with SPHINX31

All present enzymatic activity of Crystal Structure of SRPK1 in Complex with SPHINX31:
2.7.11.1;

The structure of Crystal Structure of SRPK1 in Complex with SPHINX31, PDB code: 5my8 was solved by A.Chaikuad, F.Von Delft, C.Bountra, C.H.Arrowsmith, A.M.Edwards, S.Knapp, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.74 / 1.70
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	74.883, 74.883, 310.129, 90.00, 90.00, 120.00
R / Rfree (%)	16.4 / 20

The binding sites of Fluorine atom in the Crystal Structure of SRPK1 in Complex with SPHINX31 (pdb code 5my8). 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 SRPK1 in Complex with SPHINX31, PDB code: 5my8:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of SRPK1 in Complex with SPHINX31


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 SRPK1 in Complex with SPHINX31 within 5.0Å range: probe atom residue distance (Å) B Occ A:F724 b:43.8 occ:1.00 F2 A:RXZ724 0.0 43.8 1.0 C26 A:RXZ724 1.3 37.0 1.0 F1 A:RXZ724 2.1 43.9 1.0 F A:RXZ724 2.1 42.2 1.0 C13 A:RXZ724 2.3 27.9 1.0 C14 A:RXZ724 2.7 23.2 1.0 CD1 A:ILE228 3.1 31.4 0.5 C12 A:RXZ724 3.6 26.7 1.0 CG1 A:VAL167 3.9 27.4 1.0 CG2 A:VAL223 4.0 29.4 1.0 C15 A:RXZ724 4.1 21.7 1.0 CD1 A:LEU231 4.2 39.9 1.0 CD2 A:LEU86 4.2 28.4 1.0 CG1 A:ILE228 4.3 31.3 0.5 CA A:GLY169 4.4 21.3 1.0 CD1 A:LEU86 4.4 26.1 1.0 CG1 A:ILE228 4.5 31.5 0.5 O1 A:RXZ724 4.5 22.0 1.0 O A:LEU168 4.6 23.8 1.0 CE2 A:TYR227 4.6 36.8 1.0 C11 A:RXZ724 4.7 25.4 1.0 CD2 A:TYR227 4.8 36.6 1.0 N A:GLY169 4.8 21.0 1.0 C A:LEU168 4.9 21.6 1.0 CG A:LEU86 4.9 26.6 1.0 CG1 A:VAL223 4.9 31.3 1.0 C10 A:RXZ724 5.0 22.7 1.0 CD1 A:ILE228 5.0 31.3 0.5

Fluorine binding site 2 out of 3 in the Crystal Structure of SRPK1 in Complex with SPHINX31


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 SRPK1 in Complex with SPHINX31 within 5.0Å range: probe atom residue distance (Å) B Occ A:F724 b:42.2 occ:1.00 F A:RXZ724 0.0 42.2 1.0 C26 A:RXZ724 1.3 37.0 1.0 F1 A:RXZ724 2.1 43.9 1.0 F2 A:RXZ724 2.1 43.8 1.0 C13 A:RXZ724 2.3 27.9 1.0 C12 A:RXZ724 2.8 26.7 1.0 CD1 A:LEU231 3.2 39.9 1.0 C1 A:EDO716 3.3 65.5 1.0 C14 A:RXZ724 3.5 23.2 1.0 CE2 A:TYR227 3.6 36.8 1.0 CD2 A:LEU86 3.7 28.4 1.0 C11 A:RXZ724 4.2 25.4 1.0 C2 A:EDO716 4.2 66.3 1.0 CD2 A:TYR227 4.3 36.6 1.0 O1 A:EDO716 4.4 66.5 1.0 CD1 A:ILE228 4.4 31.4 0.5 NE2 A:HIS170 4.4 34.2 1.0 CE1 A:HIS170 4.5 33.4 1.0 OH A:TYR227 4.5 48.8 1.0 CZ A:TYR227 4.5 41.6 1.0 CG A:LEU231 4.5 39.3 1.0 O2 A:EDO716 4.6 71.3 1.0 C15 A:RXZ724 4.7 21.7 1.0 CG A:LEU86 4.8 26.6 1.0 CD1 A:LEU86 4.9 26.1 1.0 C10 A:RXZ724 4.9 22.7 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of SRPK1 in Complex with SPHINX31


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 SRPK1 in Complex with SPHINX31 within 5.0Å range: probe atom residue distance (Å) B Occ A:F724 b:43.9 occ:1.00 F1 A:RXZ724 0.0 43.9 1.0 C26 A:RXZ724 1.3 37.0 1.0 F A:RXZ724 2.1 42.2 1.0 F2 A:RXZ724 2.1 43.8 1.0 C13 A:RXZ724 2.3 27.9 1.0 C12 A:RXZ724 3.1 26.7 1.0 C14 A:RXZ724 3.3 23.2 1.0 CG1 A:VAL223 3.3 31.3 1.0 CA A:GLY169 3.5 21.3 1.0 CG2 A:VAL223 3.5 29.4 1.0 CE2 A:TYR227 3.6 36.8 1.0 NE2 A:HIS170 3.9 34.2 1.0 CD2 A:HIS170 4.0 31.8 1.0 CB A:VAL223 4.1 30.3 1.0 CD2 A:TYR227 4.1 36.6 1.0 C A:GLY169 4.1 21.0 1.0 N A:HIS170 4.2 21.9 1.0 CD1 A:ILE228 4.3 31.4 0.5 C11 A:RXZ724 4.3 25.4 1.0 CE1 A:HIS170 4.4 33.4 1.0 O A:LEU168 4.5 23.8 1.0 C15 A:RXZ724 4.5 21.7 1.0 N A:GLY169 4.5 21.0 1.0 CZ A:TYR227 4.6 41.6 1.0 CG A:HIS170 4.6 29.0 1.0 C1 A:EDO716 4.8 65.5 1.0 CD1 A:LEU231 4.8 39.9 1.0 ND1 A:HIS170 4.8 32.1 1.0 OH A:TYR227 4.8 48.8 1.0 C A:LEU168 4.9 21.6 1.0 C10 A:RXZ724 4.9 22.7 1.0 O A:GLY169 5.0 21.0 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