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Fluorine in PDB 4jln: Human Dck C4S-S74E Mutant in Complex with Udp and the F2.4.1 Inhibitor (2-[({2-[3-(2-Fluoroethoxy)-4-Methoxyphenyl]-5-Propyl-1,3-Thiazol-4- Yl}Methyl)Sulfanyl]Pyrimidine-4,6-Diamine)

Enzymatic activity of Human Dck C4S-S74E Mutant in Complex with Udp and the F2.4.1 Inhibitor (2-[({2-[3-(2-Fluoroethoxy)-4-Methoxyphenyl]-5-Propyl-1,3-Thiazol-4- Yl}Methyl)Sulfanyl]Pyrimidine-4,6-Diamine)

All present enzymatic activity of Human Dck C4S-S74E Mutant in Complex with Udp and the F2.4.1 Inhibitor (2-[({2-[3-(2-Fluoroethoxy)-4-Methoxyphenyl]-5-Propyl-1,3-Thiazol-4- Yl}Methyl)Sulfanyl]Pyrimidine-4,6-Diamine):
2.7.1.74;

Protein crystallography data

The structure of Human Dck C4S-S74E Mutant in Complex with Udp and the F2.4.1 Inhibitor (2-[({2-[3-(2-Fluoroethoxy)-4-Methoxyphenyl]-5-Propyl-1,3-Thiazol-4- Yl}Methyl)Sulfanyl]Pyrimidine-4,6-Diamine), PDB code: 4jln was solved by J.Nomme, A.Lavie, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.50 / 2.15
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 68.650, 68.650, 120.050, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 25

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Human Dck C4S-S74E Mutant in Complex with Udp and the F2.4.1 Inhibitor (2-[({2-[3-(2-Fluoroethoxy)-4-Methoxyphenyl]-5-Propyl-1,3-Thiazol-4- Yl}Methyl)Sulfanyl]Pyrimidine-4,6-Diamine) (pdb code 4jln). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Human Dck C4S-S74E Mutant in Complex with Udp and the F2.4.1 Inhibitor (2-[({2-[3-(2-Fluoroethoxy)-4-Methoxyphenyl]-5-Propyl-1,3-Thiazol-4- Yl}Methyl)Sulfanyl]Pyrimidine-4,6-Diamine), PDB code: 4jln:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 4jln

Go back to Fluorine Binding Sites List in 4jln
Fluorine binding site 1 out of 2 in the Human Dck C4S-S74E Mutant in Complex with Udp and the F2.4.1 Inhibitor (2-[({2-[3-(2-Fluoroethoxy)-4-Methoxyphenyl]-5-Propyl-1,3-Thiazol-4- Yl}Methyl)Sulfanyl]Pyrimidine-4,6-Diamine)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Human Dck C4S-S74E Mutant in Complex with Udp and the F2.4.1 Inhibitor (2-[({2-[3-(2-Fluoroethoxy)-4-Methoxyphenyl]-5-Propyl-1,3-Thiazol-4- Yl}Methyl)Sulfanyl]Pyrimidine-4,6-Diamine) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:47.4
occ:1.00
 FAE A:18V301 0.0 47.4 1.0
CAK A:18V301 1.5 44.2 1.0
CAL A:18V301 2.5 43.2 1.0
OAS A:18V301 2.9 44.2 1.0
CB A:SER144 3.9 47.0 0.5
CB A:SER144 3.9 45.8 0.5
CBA A:18V301 4.1 43.7 1.0
OG A:SER144 4.2 48.1 0.5
OG A:SER144 4.5 44.2 0.5
OAR A:18V301 4.6 46.0 1.0
CE1 A:TYR204 4.7 49.4 1.0
CD1 A:TYR204 4.7 50.9 1.0
OG A:SER146 4.7 41.3 1.0
O A:SER144 4.8 44.5 1.0
NZ A:LYS207 4.9 48.4 1.0
OE2 A:GLU203 4.9 50.2 1.0
CAZ A:18V301 4.9 43.2 1.0
CAI A:18V301 5.0 44.0 1.0

Fluorine binding site 2 out of 2 in 4jln

Go back to Fluorine Binding Sites List in 4jln
Fluorine binding site 2 out of 2 in the Human Dck C4S-S74E Mutant in Complex with Udp and the F2.4.1 Inhibitor (2-[({2-[3-(2-Fluoroethoxy)-4-Methoxyphenyl]-5-Propyl-1,3-Thiazol-4- Yl}Methyl)Sulfanyl]Pyrimidine-4,6-Diamine)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Human Dck C4S-S74E Mutant in Complex with Udp and the F2.4.1 Inhibitor (2-[({2-[3-(2-Fluoroethoxy)-4-Methoxyphenyl]-5-Propyl-1,3-Thiazol-4- Yl}Methyl)Sulfanyl]Pyrimidine-4,6-Diamine) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F301

b:47.6
occ:1.00
 FAE B:18V301 0.0 47.6 1.0
CAK B:18V301 1.4 41.5 1.0
CAL B:18V301 2.3 42.4 1.0
OAS B:18V301 2.7 40.3 1.0
OG B:SER144 3.0 41.1 0.5
CB B:SER144 3.9 41.5 0.5
CE1 B:TYR204 3.9 47.3 1.0
CB B:SER144 4.0 40.6 0.5
CBA B:18V301 4.1 40.6 1.0
CD1 B:TYR204 4.2 48.4 1.0
OG B:SER144 4.4 38.4 0.5
OG B:SER146 4.6 39.1 1.0
CD2 B:LEU141 4.8 33.4 1.0
CAI B:18V301 4.8 40.2 1.0
OAR B:18V301 4.8 41.5 1.0
CZ B:TYR204 5.0 48.3 1.0
CAZ B:18V301 5.0 40.8 1.0

Reference:

J.Nomme, J.M.Murphy, Y.Su, N.D.Sansone, A.L.Armijo, S.T.Olson, C.Radu, A.Lavie. Structural Characterization of New Deoxycytidine Kinase Inhibitors Rationalizes the Affinity-Determining Moieties of the Molecules. Acta Crystallogr.,Sect.D V. 70 68 2014.
ISSN: ISSN 0907-4449
PubMed: 24419380
DOI: 10.1107/S1399004713025030
Page generated: Thu Aug 1 02:54:50 2024

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