Atomistry » Fluorine » PDB 4j0v-4jps » 4jlj
Atomistry »
  Fluorine »
    PDB 4j0v-4jps »
      4jlj »

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

Go back to Fluorine Binding Sites List in 4jlj
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

Go back to Fluorine Binding Sites List in 4jlj
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: Thu Aug 1 02:51:40 2024

Last articles

Cl in 3NG3
Cl in 3NF9
Cl in 3NFZ
Cl in 3NF7
Cl in 3NDM
Cl in 3NDU
Cl in 3NDT
Cl in 3NF6
Cl in 3NEA
Cl in 3NDX
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy