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Fluorine in PDB 4q1e: Human Dck C4S-S74E Mutant in Complex with Udp and the Inhibitor 10 {2- {[(1R/S)-1-{2-[3-(2-Fluoroethoxy)-4-Methoxyphenyl]-5-Methyl-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 10 {2- {[(1R/S)-1-{2-[3-(2-Fluoroethoxy)-4-Methoxyphenyl]-5-Methyl-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 10 {2- {[(1R/S)-1-{2-[3-(2-Fluoroethoxy)-4-Methoxyphenyl]-5-Methyl-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 10 {2- {[(1R/S)-1-{2-[3-(2-Fluoroethoxy)-4-Methoxyphenyl]-5-Methyl-1,3- Thiazol 4-Yl}Ethyl]Sulfanyl}Pyrimidine-4,6-Diamine}, PDB code: 4q1e 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) 27.92 / 1.85
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 68.736, 68.736, 122.206, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / 21.8

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Human Dck C4S-S74E Mutant in Complex with Udp and the Inhibitor 10 {2- {[(1R/S)-1-{2-[3-(2-Fluoroethoxy)-4-Methoxyphenyl]-5-Methyl-1,3- Thiazol 4-Yl}Ethyl]Sulfanyl}Pyrimidine-4,6-Diamine} (pdb code 4q1e). 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 Inhibitor 10 {2- {[(1R/S)-1-{2-[3-(2-Fluoroethoxy)-4-Methoxyphenyl]-5-Methyl-1,3- Thiazol 4-Yl}Ethyl]Sulfanyl}Pyrimidine-4,6-Diamine}, PDB code: 4q1e:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 4q1e

Go back to Fluorine Binding Sites List in 4q1e
Fluorine binding site 1 out of 4 in the Human Dck C4S-S74E Mutant in Complex with Udp and the Inhibitor 10 {2- {[(1R/S)-1-{2-[3-(2-Fluoroethoxy)-4-Methoxyphenyl]-5-Methyl-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 10 {2- {[(1R/S)-1-{2-[3-(2-Fluoroethoxy)-4-Methoxyphenyl]-5-Methyl-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:53.3
occ:1.00
 FAF A:2Y8301 0.0 53.3 1.0
CAK A:2Y8301 1.3 53.7 1.0
CAL A:2Y8301 2.2 54.3 1.0
OG A:SER144 2.6 30.2 0.5
OG A:SER144 2.9 38.5 0.5
CB A:SER144 2.9 34.7 0.5
CB A:SER144 3.0 38.3 0.5
OD1 A:ASN140 3.4 37.0 1.0
OAQ A:2Y8301 3.4 51.1 1.0
CD2 A:LEU141 3.5 29.1 1.0
O A:ASN140 3.7 32.0 1.0
CA A:LEU141 3.9 30.0 1.0
CE1 A:TYR204 3.9 37.5 1.0
C A:ASN140 4.0 33.6 1.0
N A:LEU141 4.1 30.6 1.0
CG A:ASN140 4.1 34.7 1.0
OG A:SER146 4.2 37.4 1.0
CA A:SER144 4.4 33.8 0.5
CA A:SER144 4.4 35.5 0.5
O A:HOH460 4.5 35.6 1.0
CAY A:2Y8301 4.5 47.0 1.0
CD1 A:TYR204 4.5 37.5 1.0
CG A:LEU141 4.5 29.1 1.0
CB A:LEU141 4.7 30.2 1.0
N A:SER144 4.7 33.2 1.0
ND2 A:ASN140 4.7 35.0 1.0
CAJ A:2Y8301 4.8 43.5 1.0
CB A:ASN140 4.8 33.1 1.0
C A:LEU141 4.9 30.2 1.0
CZ A:TYR204 4.9 40.5 1.0
OH A:TYR204 5.0 47.6 1.0

Fluorine binding site 2 out of 4 in 4q1e

Go back to Fluorine Binding Sites List in 4q1e
Fluorine binding site 2 out of 4 in the Human Dck C4S-S74E Mutant in Complex with Udp and the Inhibitor 10 {2- {[(1R/S)-1-{2-[3-(2-Fluoroethoxy)-4-Methoxyphenyl]-5-Methyl-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 10 {2- {[(1R/S)-1-{2-[3-(2-Fluoroethoxy)-4-Methoxyphenyl]-5-Methyl-1,3- Thiazol 4-Yl}Ethyl]Sulfanyl}Pyrimidine-4,6-Diamine} within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F302

b:52.1
occ:1.00
 FAF A:2Y7302 0.0 52.1 1.0
CAK A:2Y7302 1.2 47.8 1.0
CAL A:2Y7302 2.2 45.2 1.0
OH A:TYR86 3.1 55.8 1.0
OAQ A:2Y7302 3.3 45.5 1.0
CZ A:TYR86 3.9 51.1 1.0
CAY A:2Y7302 4.5 44.3 1.0
CE2 A:TYR86 4.5 48.4 1.0
O A:GLY199 4.7 40.5 1.0
CE1 A:TYR86 4.8 51.2 1.0

Fluorine binding site 3 out of 4 in 4q1e

Go back to Fluorine Binding Sites List in 4q1e
Fluorine binding site 3 out of 4 in the Human Dck C4S-S74E Mutant in Complex with Udp and the Inhibitor 10 {2- {[(1R/S)-1-{2-[3-(2-Fluoroethoxy)-4-Methoxyphenyl]-5-Methyl-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 3 of Human Dck C4S-S74E Mutant in Complex with Udp and the Inhibitor 10 {2- {[(1R/S)-1-{2-[3-(2-Fluoroethoxy)-4-Methoxyphenyl]-5-Methyl-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:54.5
occ:1.00
 FAF B:2Y8301 0.0 54.5 1.0
CAK B:2Y8301 1.2 50.4 1.0
CAL B:2Y8301 2.2 48.6 1.0
OG B:SER144 3.0 32.9 0.5
CB B:SER144 3.3 35.8 0.5
OAQ B:2Y8301 3.3 43.8 1.0
CB B:SER144 3.3 37.2 0.5
OG B:SER144 3.5 35.6 0.5
OG B:SER146 4.3 36.2 1.0
CE1 B:TYR204 4.4 45.4 1.0
CAY B:2Y8301 4.5 43.0 1.0
CD1 B:TYR204 4.6 49.0 1.0
CA B:SER144 4.7 35.8 0.5
CAA B:2Y7302 4.7 41.0 1.0
CA B:SER144 4.7 35.1 0.5
O B:SER144 4.8 38.4 1.0
O B:HOH424 4.9 38.3 1.0
NZ B:LYS207 5.0 55.0 1.0

Fluorine binding site 4 out of 4 in 4q1e

Go back to Fluorine Binding Sites List in 4q1e
Fluorine binding site 4 out of 4 in the Human Dck C4S-S74E Mutant in Complex with Udp and the Inhibitor 10 {2- {[(1R/S)-1-{2-[3-(2-Fluoroethoxy)-4-Methoxyphenyl]-5-Methyl-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 4 of Human Dck C4S-S74E Mutant in Complex with Udp and the Inhibitor 10 {2- {[(1R/S)-1-{2-[3-(2-Fluoroethoxy)-4-Methoxyphenyl]-5-Methyl-1,3- Thiazol 4-Yl}Ethyl]Sulfanyl}Pyrimidine-4,6-Diamine} within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F302

b:61.2
occ:1.00
 FAF B:2Y7302 0.0 61.2 1.0
CAK B:2Y7302 1.4 59.2 1.0
CAL B:2Y7302 2.3 54.9 1.0
OAQ B:2Y7302 2.5 52.2 1.0
OH B:TYR86 2.8 49.1 1.0
CZ B:TYR86 3.4 46.0 1.0
CAY B:2Y7302 3.8 45.9 1.0
CE2 B:TYR86 3.9 44.6 1.0
CE1 B:TYR86 4.2 45.5 1.0
CAJ B:2Y7302 4.4 42.7 1.0
CAA B:2Y8301 4.5 40.3 1.0
O B:GLY199 4.8 43.6 1.0
CAX B:2Y7302 4.9 43.5 1.0
OAP B:2Y7302 4.9 42.0 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. 2014.
ISSN: ISSN 0022-2623
PubMed: 25341194
DOI: 10.1021/JM501124J
Page generated: Thu Aug 1 05:08:51 2024

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