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Fluorine in PDB 4q1d: Human Dck C4S-S74E Mutant in Complex with Udp and the Inhibitor 9 {2- {[(1R)-1-{2-[3-(2-Fluoroethoxy)-4-Methoxyphenyl]-5-Propyl-1,3- Thiazol-4-Yl}Ethyl]Sulfanyl}Pyrimidine-4,6-Diamine}

Enzymatic activity of Human Dck C4S-S74E Mutant in Complex with Udp and the Inhibitor 9 {2- {[(1R)-1-{2-[3-(2-Fluoroethoxy)-4-Methoxyphenyl]-5-Propyl-1,3- Thiazol-4-Yl}Ethyl]Sulfanyl}Pyrimidine-4,6-Diamine}

All present enzymatic activity of Human Dck C4S-S74E Mutant in Complex with Udp and the Inhibitor 9 {2- {[(1R)-1-{2-[3-(2-Fluoroethoxy)-4-Methoxyphenyl]-5-Propyl-1,3- Thiazol-4-Yl}Ethyl]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 Inhibitor 9 {2- {[(1R)-1-{2-[3-(2-Fluoroethoxy)-4-Methoxyphenyl]-5-Propyl-1,3- Thiazol-4-Yl}Ethyl]Sulfanyl}Pyrimidine-4,6-Diamine}, PDB code: 4q1d 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) 27.39 / 2.00
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 68.734, 68.734, 120.623, 90.00, 90.00, 90.00
R / Rfree (%) 19.1 / 25.4

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Human Dck C4S-S74E Mutant in Complex with Udp and the Inhibitor 9 {2- {[(1R)-1-{2-[3-(2-Fluoroethoxy)-4-Methoxyphenyl]-5-Propyl-1,3- Thiazol-4-Yl}Ethyl]Sulfanyl}Pyrimidine-4,6-Diamine} (pdb code 4q1d). 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 Inhibitor 9 {2- {[(1R)-1-{2-[3-(2-Fluoroethoxy)-4-Methoxyphenyl]-5-Propyl-1,3- Thiazol-4-Yl}Ethyl]Sulfanyl}Pyrimidine-4,6-Diamine}, PDB code: 4q1d:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 4q1d

Go back to Fluorine Binding Sites List in 4q1d
Fluorine binding site 1 out of 2 in the Human Dck C4S-S74E Mutant in Complex with Udp and the Inhibitor 9 {2- {[(1R)-1-{2-[3-(2-Fluoroethoxy)-4-Methoxyphenyl]-5-Propyl-1,3- Thiazol-4-Yl}Ethyl]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 Inhibitor 9 {2- {[(1R)-1-{2-[3-(2-Fluoroethoxy)-4-Methoxyphenyl]-5-Propyl-1,3- Thiazol-4-Yl}Ethyl]Sulfanyl}Pyrimidine-4,6-Diamine} within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:66.8
occ:1.00
 FAF A:2Y1301 0.0 66.8 1.0
CAL A:2Y1301 1.4 67.9 1.0
CAM A:2Y1301 2.3 62.0 1.0
OG A:SER144 2.5 57.7 0.5
CB A:SER144 3.0 51.4 0.5
CB A:SER144 3.0 54.1 0.5
OG A:SER144 3.2 50.9 0.5
CE1 A:TYR204 3.3 65.4 1.0
OAS A:2Y1301 3.5 55.9 1.0
OD1 A:ASN140 3.8 42.0 1.0
CD2 A:LEU141 4.0 49.6 1.0
CD1 A:TYR204 4.1 64.6 1.0
O A:ASN140 4.2 46.9 1.0
OG A:SER146 4.2 45.8 1.0
CZ A:TYR204 4.3 63.7 1.0
OH A:TYR204 4.4 58.1 1.0
CA A:LEU141 4.5 44.9 1.0
CA A:SER144 4.5 49.1 0.5
CA A:SER144 4.5 50.4 0.5
CAZ A:2Y1301 4.6 62.0 1.0
CG A:ASN140 4.7 46.4 1.0
C A:ASN140 4.7 51.6 1.0
O A:SER144 4.9 48.2 1.0
N A:LEU141 4.9 49.0 1.0

Fluorine binding site 2 out of 2 in 4q1d

Go back to Fluorine Binding Sites List in 4q1d
Fluorine binding site 2 out of 2 in the Human Dck C4S-S74E Mutant in Complex with Udp and the Inhibitor 9 {2- {[(1R)-1-{2-[3-(2-Fluoroethoxy)-4-Methoxyphenyl]-5-Propyl-1,3- Thiazol-4-Yl}Ethyl]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 Inhibitor 9 {2- {[(1R)-1-{2-[3-(2-Fluoroethoxy)-4-Methoxyphenyl]-5-Propyl-1,3- Thiazol-4-Yl}Ethyl]Sulfanyl}Pyrimidine-4,6-Diamine} within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F301

b:60.6
occ:1.00
 FAF B:2Y1301 0.0 60.6 1.0
CAL B:2Y1301 1.3 57.6 1.0
OAS B:2Y1301 2.2 54.3 1.0
CAM B:2Y1301 2.2 55.7 1.0
CAZ B:2Y1301 3.6 54.6 1.0
OG B:SER144 3.6 47.0 0.5
CB B:SER144 3.8 48.6 0.5
CB B:SER144 3.9 43.8 0.5
OG B:SER144 3.9 39.0 0.5
CE1 B:TYR204 4.1 63.0 1.0
CD1 B:TYR204 4.3 56.3 1.0
CAJ B:2Y1301 4.3 56.6 1.0
OAR B:2Y1301 4.4 57.6 1.0
CAY B:2Y1301 4.5 54.6 1.0
OD1 B:ASN140 4.7 47.5 1.0
CD2 B:LEU141 4.8 44.5 1.0
CZ B:TYR204 4.9 63.5 1.0
OG B:SER146 4.9 44.4 1.0

Reference:

J.Nomme, Z.Li, R.M.Gipson, J.Wang, A.L.Armijo, T.Le, S.Poddar, T.Smith, B.D.Santarsiero, H.A.Nguyen, J.Czernin, A.N.Alexandrova, M.E.Jung, C.G.Radu, A.Lavie. Structure-Guided Development of Deoxycytidine Kinase Inhibitors with Nanomolar Affinity and Improved Metabolic Stability. J.Med.Chem. V. 57 9480 2014.
ISSN: ISSN 0022-2623
PubMed: 25341194
DOI: 10.1021/JM501124J
Page generated: Tue Jul 15 00:18:00 2025

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