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Fluorine in PDB 4jlk: Human Dck C4S-S74E Mutant in Complex with Udp and the F2.2.1 Inhibitor (2-[({2-[3-(2-Fluoroethoxy)-4-Methoxyphenyl]-5-Methyl-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 F2.2.1 Inhibitor (2-[({2-[3-(2-Fluoroethoxy)-4-Methoxyphenyl]-5-Methyl-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 F2.2.1 Inhibitor (2-[({2-[3-(2-Fluoroethoxy)-4-Methoxyphenyl]-5-Methyl-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 F2.2.1 Inhibitor (2-[({2-[3-(2-Fluoroethoxy)-4-Methoxyphenyl]-5-Methyl-1,3-Thiazol-4- Yl}Methyl)Sulfanyl]Pyrimidine-4,6-Diamine), PDB code: 4jlk 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) 29.73 / 1.89
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 68.600, 68.600, 120.706, 90.00, 90.00, 90.00
R / Rfree (%) 16.7 / 21.5

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Human Dck C4S-S74E Mutant in Complex with Udp and the F2.2.1 Inhibitor (2-[({2-[3-(2-Fluoroethoxy)-4-Methoxyphenyl]-5-Methyl-1,3-Thiazol-4- Yl}Methyl)Sulfanyl]Pyrimidine-4,6-Diamine) (pdb code 4jlk). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Human Dck C4S-S74E Mutant in Complex with Udp and the F2.2.1 Inhibitor (2-[({2-[3-(2-Fluoroethoxy)-4-Methoxyphenyl]-5-Methyl-1,3-Thiazol-4- Yl}Methyl)Sulfanyl]Pyrimidine-4,6-Diamine), PDB code: 4jlk:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 4jlk

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Fluorine binding site 1 out of 4 in the Human Dck C4S-S74E Mutant in Complex with Udp and the F2.2.1 Inhibitor (2-[({2-[3-(2-Fluoroethoxy)-4-Methoxyphenyl]-5-Methyl-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 F2.2.1 Inhibitor (2-[({2-[3-(2-Fluoroethoxy)-4-Methoxyphenyl]-5-Methyl-1,3-Thiazol-4- Yl}Methyl)Sulfanyl]Pyrimidine-4,6-Diamine) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F402

b:54.3
occ:1.00
 FAN A:1NO402 0.0 54.3 1.0
CAM A:1NO402 1.4 51.8 1.0
CAL A:1NO402 2.4 49.8 1.0
OG A:SER144 2.7 37.7 0.5
OG A:SER144 3.0 31.5 0.5
CE1 A:TYR204 3.1 35.9 1.0
OAK A:1NO402 3.3 43.1 1.0
CB A:SER144 3.3 30.9 0.5
CB A:SER144 3.4 33.6 0.5
OD1 A:ASN140 3.5 33.7 1.0
CD1 A:TYR204 3.8 36.7 1.0
CZ A:TYR204 4.2 38.3 1.0
O A:ASN140 4.2 30.2 1.0
OH A:TYR204 4.3 34.9 1.0
CD2 A:LEU141 4.3 29.1 1.0
CAV A:1NO402 4.4 43.4 1.0
CG A:ASN140 4.5 33.0 1.0
CA A:LEU141 4.6 28.1 1.0
C A:ASN140 4.7 31.2 1.0
CA A:SER144 4.8 32.6 0.5
N A:LEU141 4.8 29.5 1.0
CA A:SER144 4.8 33.9 0.5
CAU A:1NO402 4.9 40.9 1.0
O A:HOH521 4.9 26.5 1.0

Fluorine binding site 2 out of 4 in 4jlk

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Fluorine binding site 2 out of 4 in the Human Dck C4S-S74E Mutant in Complex with Udp and the F2.2.1 Inhibitor (2-[({2-[3-(2-Fluoroethoxy)-4-Methoxyphenyl]-5-Methyl-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 F2.2.1 Inhibitor (2-[({2-[3-(2-Fluoroethoxy)-4-Methoxyphenyl]-5-Methyl-1,3-Thiazol-4- Yl}Methyl)Sulfanyl]Pyrimidine-4,6-Diamine) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F403

b:55.2
occ:1.00
 FAN A:1NO403 0.0 55.2 1.0
CAM A:1NO403 1.4 53.9 1.0
CAL A:1NO403 2.4 51.7 1.0
O A:GLY199 2.6 43.0 1.0
OAK A:1NO403 3.1 49.3 1.0
C A:GLY199 3.3 42.5 1.0
CA A:GLY199 3.4 39.7 1.0
OH A:TYR86 4.0 42.3 1.0
O A:HOH581 4.1 44.7 1.0
CAV A:1NO403 4.3 46.0 1.0
N A:ILE200 4.6 40.1 1.0
N A:GLY199 4.6 39.0 1.0
CAU A:1NO403 4.7 43.7 1.0
CZ A:TYR86 5.0 38.2 1.0
CD A:PRO201 5.0 40.5 1.0

Fluorine binding site 3 out of 4 in 4jlk

Go back to Fluorine Binding Sites List in 4jlk
Fluorine binding site 3 out of 4 in the Human Dck C4S-S74E Mutant in Complex with Udp and the F2.2.1 Inhibitor (2-[({2-[3-(2-Fluoroethoxy)-4-Methoxyphenyl]-5-Methyl-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 3 of Human Dck C4S-S74E Mutant in Complex with Udp and the F2.2.1 Inhibitor (2-[({2-[3-(2-Fluoroethoxy)-4-Methoxyphenyl]-5-Methyl-1,3-Thiazol-4- Yl}Methyl)Sulfanyl]Pyrimidine-4,6-Diamine) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F402

b:40.2
occ:1.00
 FAN B:1NO402 0.0 40.2 1.0
CAM B:1NO402 1.4 37.8 1.0
CAL B:1NO402 2.3 36.4 1.0
OAK B:1NO402 2.6 32.6 1.0
CAY B:1NO403 3.5 42.1 1.0
OG B:SER144 3.7 31.5 0.5
CB B:SER144 3.9 30.9 0.5
CB B:SER144 3.9 26.9 0.5
CAV B:1NO402 3.9 35.6 1.0
OG B:SER144 4.0 23.2 0.5
OG B:SER146 4.3 34.2 1.0
CBB B:1NO403 4.6 44.5 1.0
CAU B:1NO402 4.6 36.9 1.0
OAX B:1NO402 4.7 36.0 1.0
CD1 B:TYR204 4.8 49.0 1.0
CAW B:1NO402 4.8 37.5 1.0
OAX B:1NO403 4.9 44.5 1.0
CE1 B:TYR204 4.9 49.9 1.0
O B:HOH544 4.9 31.1 1.0

Fluorine binding site 4 out of 4 in 4jlk

Go back to Fluorine Binding Sites List in 4jlk
Fluorine binding site 4 out of 4 in the Human Dck C4S-S74E Mutant in Complex with Udp and the F2.2.1 Inhibitor (2-[({2-[3-(2-Fluoroethoxy)-4-Methoxyphenyl]-5-Methyl-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 4 of Human Dck C4S-S74E Mutant in Complex with Udp and the F2.2.1 Inhibitor (2-[({2-[3-(2-Fluoroethoxy)-4-Methoxyphenyl]-5-Methyl-1,3-Thiazol-4- Yl}Methyl)Sulfanyl]Pyrimidine-4,6-Diamine) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F403

b:46.4
occ:1.00
 FAN B:1NO403 0.0 46.4 1.0
CAM B:1NO403 1.4 50.7 1.0
CAL B:1NO403 2.4 47.2 1.0
OAK B:1NO403 2.7 48.1 1.0
CAV B:1NO403 4.1 46.5 1.0
O B:GLY199 4.5 43.1 1.0
OAX B:1NO403 4.6 44.5 1.0
CAY B:1NO402 4.7 41.7 1.0
OH B:TYR86 4.8 42.9 1.0
CAW B:1NO403 4.8 46.2 1.0
CAU B:1NO403 5.0 45.4 1.0

Reference:

J.M.Murphy, A.L.Armijo, J.Nomme, C.H.Lee, Q.A.Smith, Z.Li, D.O.Campbell, H.I.Liao, D.A.Nathanson, W.R.Austin, J.T.Lee, R.Darvish, L.Wei, J.Wang, Y.Su, R.Damoiseaux, S.Sadeghi, M.E.Phelps, H.R.Herschman, J.Czernin, A.N.Alexandrova, M.E.Jung, A.Lavie, C.G.Radu. Development of New Deoxycytidine Kinase Inhibitors and Noninvasive in Vivo Evaluation Using Positron Emission Tomography. J.Med.Chem. V. 56 6696 2013.
ISSN: ISSN 0022-2623
PubMed: 23947754
DOI: 10.1021/JM400457Y
Page generated: Sun Dec 13 12:05:28 2020

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