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Fluorine in PDB 4jlj: Human Dck C4S-S74E Mutant in Complex with Udp and the F2.1.1 Inhibitor (2-[({2-[3-(2-Fluoroethoxy)-4-Methoxyphenyl]-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 F2.1.1 Inhibitor (2-[({2-[3-(2-Fluoroethoxy)-4-Methoxyphenyl]-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 F2.1.1 Inhibitor (2-[({2-[3-(2-Fluoroethoxy)-4-Methoxyphenyl]-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 F2.1.1 Inhibitor (2-[({2-[3-(2-Fluoroethoxy)-4-Methoxyphenyl]-1,3-Thiazol-4- Yl}Methyl)Sulfanyl]Pyrimidine-4,6-Diamine), PDB code: 4jlj 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) 26.04 / 2.00
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 68.998, 68.998, 123.180, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 23

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Human Dck C4S-S74E Mutant in Complex with Udp and the F2.1.1 Inhibitor (2-[({2-[3-(2-Fluoroethoxy)-4-Methoxyphenyl]-1,3-Thiazol-4- Yl}Methyl)Sulfanyl]Pyrimidine-4,6-Diamine) (pdb code 4jlj). 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 F2.1.1 Inhibitor (2-[({2-[3-(2-Fluoroethoxy)-4-Methoxyphenyl]-1,3-Thiazol-4- Yl}Methyl)Sulfanyl]Pyrimidine-4,6-Diamine), PDB code: 4jlj:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 4jlj

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Fluorine binding site 1 out of 4 in the Human Dck C4S-S74E Mutant in Complex with Udp and the F2.1.1 Inhibitor (2-[({2-[3-(2-Fluoroethoxy)-4-Methoxyphenyl]-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 F2.1.1 Inhibitor (2-[({2-[3-(2-Fluoroethoxy)-4-Methoxyphenyl]-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:58.2
occ:1.00
 FAD A:1NM301 0.0 58.2 1.0
CAJ A:1NM301 1.6 62.3 1.0
CAK A:1NM301 2.6 57.7 1.0
CD1 A:TYR204 3.2 45.4 1.0
OD1 A:ASN140 3.5 42.2 1.0
CE1 A:TYR204 3.5 48.5 1.0
OG A:SER144 3.6 39.9 0.5
CAA A:1NM302 3.8 49.6 1.0
OAQ A:1NM301 3.8 58.3 1.0
CB A:SER144 3.9 39.3 0.5
CB A:SER144 4.0 39.6 0.5
OG A:SER144 4.0 38.2 0.5
CG A:ASN140 4.3 40.0 1.0
CG A:TYR204 4.3 47.0 1.0
CAF A:1NM302 4.4 51.5 1.0
ND2 A:ASN140 4.4 40.3 1.0
O A:ASN140 4.7 40.6 1.0
CB A:TYR204 4.8 45.4 1.0
CD A:LYS207 4.9 47.7 1.0
CZ A:TYR204 4.9 49.3 1.0
CAZ A:1NM301 4.9 56.3 1.0

Fluorine binding site 2 out of 4 in 4jlj

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Fluorine binding site 2 out of 4 in the Human Dck C4S-S74E Mutant in Complex with Udp and the F2.1.1 Inhibitor (2-[({2-[3-(2-Fluoroethoxy)-4-Methoxyphenyl]-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 F2.1.1 Inhibitor (2-[({2-[3-(2-Fluoroethoxy)-4-Methoxyphenyl]-1,3-Thiazol-4- Yl}Methyl)Sulfanyl]Pyrimidine-4,6-Diamine) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F302

b:56.1
occ:1.00
 FAD A:1NM302 0.0 56.1 1.0
CAJ A:1NM302 1.5 61.7 1.0
CAK A:1NM302 2.5 60.9 1.0
OH A:TYR86 3.1 50.7 1.0
CZ A:TYR86 3.4 52.4 1.0
CE2 A:TYR86 3.8 49.9 1.0
OAQ A:1NM302 3.8 58.0 1.0
CE1 A:TYR86 4.1 47.1 1.0
CAA A:1NM301 4.6 54.1 1.0
CD2 A:TYR86 4.7 50.5 1.0
CAZ A:1NM302 4.7 53.9 1.0
CD1 A:TYR86 4.9 51.0 1.0

Fluorine binding site 3 out of 4 in 4jlj

Go back to Fluorine Binding Sites List in 4jlj
Fluorine binding site 3 out of 4 in the Human Dck C4S-S74E Mutant in Complex with Udp and the F2.1.1 Inhibitor (2-[({2-[3-(2-Fluoroethoxy)-4-Methoxyphenyl]-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 F2.1.1 Inhibitor (2-[({2-[3-(2-Fluoroethoxy)-4-Methoxyphenyl]-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:64.9
occ:1.00
 FAD B:1NM301 0.0 64.9 1.0
CAJ B:1NM301 1.7 58.5 1.0
CAK B:1NM301 2.7 57.0 1.0
OAQ B:1NM301 2.7 55.4 1.0
OG B:SER144 2.8 44.6 0.5
OG B:SER144 3.1 41.4 0.5
CB B:SER144 3.3 43.5 0.5
CB B:SER144 3.3 44.4 0.5
OD1 B:ASN140 3.6 39.9 1.0
CD2 B:LEU141 3.9 33.5 1.0
CAZ B:1NM301 4.0 56.9 1.0
OG B:SER146 4.0 36.8 1.0
CG B:ASN140 4.3 42.2 1.0
ND2 B:ASN140 4.3 41.5 1.0
CD1 B:TYR204 4.4 44.6 1.0
CE1 B:TYR204 4.4 44.5 1.0
CAI B:1NM301 4.6 52.3 1.0
CA B:LEU141 4.7 37.0 1.0
O B:ASN140 4.7 34.9 1.0
CA B:SER144 4.8 42.2 0.5
CA B:SER144 4.8 42.7 0.5
O B:HOH441 4.8 27.5 1.0
CG B:LEU141 5.0 36.8 1.0
CB B:SER146 5.0 40.6 1.0

Fluorine binding site 4 out of 4 in 4jlj

Go back to Fluorine Binding Sites List in 4jlj
Fluorine binding site 4 out of 4 in the Human Dck C4S-S74E Mutant in Complex with Udp and the F2.1.1 Inhibitor (2-[({2-[3-(2-Fluoroethoxy)-4-Methoxyphenyl]-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 F2.1.1 Inhibitor (2-[({2-[3-(2-Fluoroethoxy)-4-Methoxyphenyl]-1,3-Thiazol-4- Yl}Methyl)Sulfanyl]Pyrimidine-4,6-Diamine) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F302

b:50.2
occ:1.00
 FAD B:1NM302 0.0 50.2 1.0
CAJ B:1NM302 1.5 56.0 1.0
CAK B:1NM302 2.4 51.1 1.0
OAQ B:1NM302 2.4 54.0 1.0
CAZ B:1NM302 3.7 52.5 1.0
O B:GLY199 3.9 50.6 1.0
OAP B:1NM302 4.2 53.9 1.0
C B:GLY199 4.3 52.0 1.0
CA B:GLY199 4.4 48.9 1.0
CAY B:1NM302 4.5 52.4 1.0
CAI B:1NM302 4.6 53.0 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: Sun Dec 13 12:05:26 2020

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