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Fluorine in PDB 5myv: Crystal Structure of SRPK2 in Complex with Compound 1

Enzymatic activity of Crystal Structure of SRPK2 in Complex with Compound 1

All present enzymatic activity of Crystal Structure of SRPK2 in Complex with Compound 1:
2.7.11.1;

Protein crystallography data

The structure of Crystal Structure of SRPK2 in Complex with Compound 1, PDB code: 5myv was solved by A.Chaikuad, A.C.W.Pike, P.Savitsky, F.Von Delft, C.Bountra, A.M.Edwards, C.H.Arrowsmith, 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) 29.87 / 2.90
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 188.790, 248.990, 146.730, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / 21.7

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Fluorine atom in the Crystal Structure of SRPK2 in Complex with Compound 1 (pdb code 5myv). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 12 binding sites of Fluorine where determined in the Crystal Structure of SRPK2 in Complex with Compound 1, PDB code: 5myv:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 12 in 5myv

Go back to Fluorine Binding Sites List in 5myv
Fluorine binding site 1 out of 12 in the Crystal Structure of SRPK2 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 SRPK2 in Complex with Compound 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F716

b:66.9
occ:1.00
 F2 A:W4A716 0.0 66.9 1.0
C13 A:W4A716 1.3 64.3 1.0
F1 A:W4A716 2.1 70.3 1.0
F A:W4A716 2.1 64.0 1.0
C12 A:W4A716 2.4 61.0 1.0
C10 A:W4A716 2.9 60.8 1.0
CE A:MET243 3.4 0.2 1.0
C11 A:W4A716 3.5 59.7 1.0
CD2 A:LEU98 3.5 66.0 1.0
CE1 A:TYR239 4.1 83.8 1.0
SD A:MET243 4.2 0.3 1.0
C9 A:W4A716 4.3 61.4 1.0
CG A:MET243 4.3 0.4 1.0
CD1 A:LEU98 4.4 67.2 1.0
CG A:LEU98 4.5 66.2 1.0
C2 A:W4A716 4.6 58.7 1.0
CD1 A:TYR239 4.6 82.6 1.0
CG1 A:VAL179 4.9 62.0 1.0
NE2 A:HIS182 4.9 67.4 1.0
C3 A:W4A716 4.9 59.3 1.0

Fluorine binding site 2 out of 12 in 5myv

Go back to Fluorine Binding Sites List in 5myv
Fluorine binding site 2 out of 12 in the Crystal Structure of SRPK2 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 SRPK2 in Complex with Compound 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F716

b:70.3
occ:1.00
 F1 A:W4A716 0.0 70.3 1.0
C13 A:W4A716 1.3 64.3 1.0
F2 A:W4A716 2.1 66.9 1.0
F A:W4A716 2.1 64.0 1.0
C12 A:W4A716 2.4 61.0 1.0
C11 A:W4A716 2.7 59.7 1.0
CG1 A:VAL179 3.1 62.0 1.0
C10 A:W4A716 3.6 60.8 1.0
C2 A:W4A716 4.1 58.7 1.0
O A:W4A716 4.3 62.5 1.0
CG2 A:VAL235 4.3 66.3 1.0
CA A:GLY181 4.4 61.6 1.0
CB A:VAL179 4.5 61.2 1.0
N A:GLY181 4.5 61.3 1.0
CG2 A:VAL240 4.6 86.1 1.0
CD1 A:LEU98 4.6 67.2 1.0
O A:LEU180 4.7 59.9 1.0
C A:LEU180 4.7 60.0 1.0
C9 A:W4A716 4.8 61.4 1.0
N A:LEU180 4.8 59.2 1.0
CD2 A:LEU98 4.8 66.0 1.0
C3 A:W4A716 4.9 59.3 1.0
N A:W4A716 5.0 61.5 1.0

Fluorine binding site 3 out of 12 in 5myv

Go back to Fluorine Binding Sites List in 5myv
Fluorine binding site 3 out of 12 in the Crystal Structure of SRPK2 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 SRPK2 in Complex with Compound 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F716

b:64.0
occ:1.00
 F A:W4A716 0.0 64.0 1.0
C13 A:W4A716 1.3 64.3 1.0
F1 A:W4A716 2.1 70.3 1.0
F2 A:W4A716 2.1 66.9 1.0
C12 A:W4A716 2.3 61.0 1.0
C10 A:W4A716 2.9 60.8 1.0
C11 A:W4A716 3.3 59.7 1.0
CE1 A:TYR239 3.6 83.8 1.0
CA A:GLY181 3.9 61.6 1.0
CG2 A:VAL235 4.0 66.3 1.0
CG1 A:VAL235 4.1 65.4 1.0
CD1 A:TYR239 4.1 82.6 1.0
NE2 A:HIS182 4.2 67.4 1.0
CD2 A:HIS182 4.2 64.5 1.0
C9 A:W4A716 4.2 61.4 1.0
C2 A:W4A716 4.5 58.7 1.0
C A:GLY181 4.5 60.6 1.0
CZ A:TYR239 4.6 83.4 1.0
N A:HIS182 4.6 61.6 1.0
N A:GLY181 4.7 61.3 1.0
CB A:VAL235 4.7 66.7 1.0
CE A:MET243 4.8 0.2 1.0
OH A:TYR239 4.8 83.0 1.0
O A:LEU180 4.8 59.9 1.0
C3 A:W4A716 4.9 59.3 1.0
CG1 A:VAL179 4.9 62.0 1.0

Fluorine binding site 4 out of 12 in 5myv

Go back to Fluorine Binding Sites List in 5myv
Fluorine binding site 4 out of 12 in the Crystal Structure of SRPK2 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 4 of Crystal Structure of SRPK2 in Complex with Compound 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F715

b:0.8
occ:1.00
 F2 B:W4A715 0.0 0.8 1.0
C13 B:W4A715 1.3 0.6 1.0
F1 B:W4A715 2.1 0.5 1.0
F B:W4A715 2.1 0.3 1.0
C12 B:W4A715 2.4 0.8 1.0
C10 B:W4A715 3.1 0.7 1.0
C11 B:W4A715 3.3 0.0 1.0
CE B:MET243 3.5 0.5 1.0
CD2 B:LEU98 3.6 0.3 1.0
CG B:MET243 3.9 0.9 1.0
C9 B:W4A715 4.4 0.7 1.0
CB B:MET243 4.4 0.5 1.0
SD B:MET243 4.4 0.1 1.0
C2 B:W4A715 4.6 0.5 1.0
CD1 B:LEU98 4.6 98.2 1.0
CG B:LEU98 4.7 100.0 1.0
CE2 B:TYR239 4.8 0.8 1.0
CG1 B:VAL179 4.8 91.2 1.0
C3 B:W4A715 5.0 0.4 1.0

Fluorine binding site 5 out of 12 in 5myv

Go back to Fluorine Binding Sites List in 5myv
Fluorine binding site 5 out of 12 in the Crystal Structure of SRPK2 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 5 of Crystal Structure of SRPK2 in Complex with Compound 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F715

b:0.5
occ:1.00
 F1 B:W4A715 0.0 0.5 1.0
C13 B:W4A715 1.3 0.6 1.0
F B:W4A715 2.1 0.3 1.0
F2 B:W4A715 2.1 0.8 1.0
C12 B:W4A715 2.4 0.8 1.0
C11 B:W4A715 2.7 0.0 1.0
CG1 B:VAL179 3.3 91.2 1.0
C10 B:W4A715 3.6 0.7 1.0
C2 B:W4A715 4.1 0.5 1.0
CA B:GLY181 4.2 87.6 1.0
O B:W4A715 4.3 92.3 1.0
CG2 B:VAL235 4.4 0.7 1.0
N B:GLY181 4.4 85.7 1.0
CG2 B:VAL240 4.5 0.6 1.0
C B:LEU180 4.7 87.8 1.0
O B:LEU180 4.7 92.6 1.0
CB B:VAL179 4.8 88.6 1.0
C9 B:W4A715 4.8 0.7 1.0
N B:LEU180 4.9 86.9 1.0
CE2 B:TYR239 4.9 0.8 1.0
C3 B:W4A715 5.0 0.4 1.0
CD2 B:TYR239 5.0 1.0 1.0

Fluorine binding site 6 out of 12 in 5myv

Go back to Fluorine Binding Sites List in 5myv
Fluorine binding site 6 out of 12 in the Crystal Structure of SRPK2 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 6 of Crystal Structure of SRPK2 in Complex with Compound 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F715

b:0.3
occ:1.00
 F B:W4A715 0.0 0.3 1.0
C13 B:W4A715 1.3 0.6 1.0
F1 B:W4A715 2.1 0.5 1.0
F2 B:W4A715 2.1 0.8 1.0
C12 B:W4A715 2.3 0.8 1.0
C10 B:W4A715 2.9 0.7 1.0
CE2 B:TYR239 3.4 0.8 1.0
C11 B:W4A715 3.5 0.0 1.0
CE B:MET243 3.8 0.5 1.0
NE2 B:HIS182 3.9 0.6 1.0
CD2 B:HIS182 3.9 0.7 1.0
CD2 B:TYR239 4.0 1.0 1.0
C9 B:W4A715 4.2 0.7 1.0
CG B:MET243 4.3 0.9 1.0
CA B:GLY181 4.3 87.6 1.0
CZ B:TYR239 4.5 0.3 1.0
C2 B:W4A715 4.7 0.5 1.0
OH B:TYR239 4.7 0.8 1.0
CG2 B:VAL235 4.7 0.7 1.0
C B:GLY181 4.7 88.9 1.0
CE1 B:HIS182 4.7 0.8 1.0
SD B:MET243 4.8 0.1 1.0
N B:HIS182 4.8 94.0 1.0
CG1 B:VAL235 4.9 0.2 1.0
CG B:HIS182 4.9 0.1 1.0
C3 B:W4A715 4.9 0.4 1.0

Fluorine binding site 7 out of 12 in 5myv

Go back to Fluorine Binding Sites List in 5myv
Fluorine binding site 7 out of 12 in the Crystal Structure of SRPK2 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 7 of Crystal Structure of SRPK2 in Complex with Compound 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F711

b:1.0
occ:1.00
 F2 C:W4A711 0.0 1.0 1.0
C13 C:W4A711 1.3 97.9 1.0
F C:W4A711 2.1 90.8 1.0
F1 C:W4A711 2.1 0.0 1.0
C12 C:W4A711 2.3 93.0 1.0
C10 C:W4A711 2.8 93.3 1.0
CE C:MET243 3.5 0.3 1.0
C11 C:W4A711 3.6 90.8 1.0
CE2 C:TYR239 3.6 88.2 1.0
CG C:MET243 3.8 0.9 1.0
SD C:MET243 4.1 0.6 1.0
C9 C:W4A711 4.1 95.3 1.0
CD2 C:TYR239 4.3 88.8 1.0
CD2 C:LEU98 4.4 88.4 1.0
NE2 C:HIS182 4.5 99.7 1.0
CB C:MET243 4.6 0.0 1.0
CZ C:TYR239 4.6 88.6 1.0
CE1 C:HIS182 4.7 98.0 1.0
OH C:TYR239 4.7 88.8 1.0
C2 C:W4A711 4.7 89.3 1.0
C3 C:W4A711 4.9 91.5 1.0

Fluorine binding site 8 out of 12 in 5myv

Go back to Fluorine Binding Sites List in 5myv
Fluorine binding site 8 out of 12 in the Crystal Structure of SRPK2 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 8 of Crystal Structure of SRPK2 in Complex with Compound 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F711

b:0.0
occ:1.00
 F1 C:W4A711 0.0 0.0 1.0
C13 C:W4A711 1.3 97.9 1.0
F2 C:W4A711 2.1 1.0 1.0
F C:W4A711 2.1 90.8 1.0
C12 C:W4A711 2.4 93.0 1.0
C11 C:W4A711 2.8 90.8 1.0
CG1 C:VAL179 3.5 93.1 1.0
C10 C:W4A711 3.6 93.3 1.0
C2 C:W4A711 4.1 89.3 1.0
O C:W4A711 4.4 78.0 1.0
CG2 C:VAL240 4.5 95.6 1.0
CD2 C:LEU98 4.6 88.4 1.0
CG2 C:VAL235 4.7 0.2 1.0
C9 C:W4A711 4.7 95.3 1.0
CD1 C:LEU98 4.7 85.4 1.0
CA C:GLY181 4.8 78.2 1.0
CE2 C:TYR239 4.9 88.2 1.0
N C:GLY181 4.9 80.3 1.0
CB C:VAL179 4.9 92.6 1.0
C3 C:W4A711 4.9 91.5 1.0
CD2 C:TYR239 5.0 88.8 1.0

Fluorine binding site 9 out of 12 in 5myv

Go back to Fluorine Binding Sites List in 5myv
Fluorine binding site 9 out of 12 in the Crystal Structure of SRPK2 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 9 of Crystal Structure of SRPK2 in Complex with Compound 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F711

b:90.8
occ:1.00
 F C:W4A711 0.0 90.8 1.0
C13 C:W4A711 1.3 97.9 1.0
F2 C:W4A711 2.1 1.0 1.0
F1 C:W4A711 2.1 0.0 1.0
C12 C:W4A711 2.3 93.0 1.0
C10 C:W4A711 3.2 93.3 1.0
C11 C:W4A711 3.2 90.8 1.0
CE2 C:TYR239 3.6 88.2 1.0
CA C:GLY181 3.6 78.2 1.0
CG2 C:VAL235 3.8 0.2 1.0
CD2 C:TYR239 3.9 88.8 1.0
CG1 C:VAL235 4.0 99.3 1.0
C C:GLY181 4.2 75.3 1.0
NE2 C:HIS182 4.3 99.7 1.0
N C:GLY181 4.3 80.3 1.0
CD2 C:HIS182 4.4 93.7 1.0
C9 C:W4A711 4.4 95.3 1.0
C2 C:W4A711 4.5 89.3 1.0
N C:HIS182 4.5 75.4 1.0
O C:LEU180 4.5 91.2 1.0
CB C:VAL235 4.5 0.4 1.0
C C:LEU180 4.7 84.6 1.0
CZ C:TYR239 4.8 88.6 1.0
CE1 C:HIS182 4.8 98.0 1.0
CG1 C:VAL179 4.9 93.1 1.0
C3 C:W4A711 4.9 91.5 1.0
CG C:HIS182 5.0 88.5 1.0
O C:GLY181 5.0 73.0 1.0

Fluorine binding site 10 out of 12 in 5myv

Go back to Fluorine Binding Sites List in 5myv
Fluorine binding site 10 out of 12 in the Crystal Structure of SRPK2 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 10 of Crystal Structure of SRPK2 in Complex with Compound 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F710

b:87.3
occ:1.00
 F2 D:W4A710 0.0 87.3 1.0
C13 D:W4A710 1.3 88.0 1.0
F1 D:W4A710 2.1 92.3 1.0
F D:W4A710 2.1 89.9 1.0
C12 D:W4A710 2.4 84.7 1.0
C11 D:W4A710 2.8 77.7 1.0
CG1 D:VAL179 3.4 89.3 1.0
C10 D:W4A710 3.6 83.8 1.0
C2 D:W4A710 4.1 74.8 1.0
CD2 D:LEU98 4.3 90.9 1.0
CE D:MET243 4.3 0.9 1.0
CD1 D:LEU98 4.4 85.2 1.0
O D:W4A710 4.5 75.4 1.0
CG2 D:VAL235 4.5 96.2 1.0
CA D:GLY181 4.5 92.1 1.0
N D:GLY181 4.7 89.9 1.0
O D:LEU180 4.7 99.3 1.0
C9 D:W4A710 4.8 85.0 1.0
CE2 D:TYR239 4.8 0.7 1.0
C D:LEU180 4.8 92.0 1.0
CB D:VAL179 4.9 88.4 1.0
CG D:LEU98 4.9 87.0 1.0
C3 D:W4A710 5.0 79.7 1.0
CG2 D:VAL240 5.0 99.5 1.0

Reference:

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
Page generated: Thu Aug 1 11:53:25 2024

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