Atomistry » Fluorine » PDB 4kbk-4l3l » 4ky8
Atomistry »
  Fluorine »
    PDB 4kbk-4l3l »
      4ky8 »

Fluorine in PDB 4ky8: Crystal Structure of Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Methotrexate, Fdump and 4-((2-Amino-6-Methyl-4-Oxo-4,7- Dihydro-3H-Pyrrolo[2,3-D]Pyrimidin-5-Yl)Thio)-2-Chlorophenyl)-L- Glutamic Acid

Enzymatic activity of Crystal Structure of Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Methotrexate, Fdump and 4-((2-Amino-6-Methyl-4-Oxo-4,7- Dihydro-3H-Pyrrolo[2,3-D]Pyrimidin-5-Yl)Thio)-2-Chlorophenyl)-L- Glutamic Acid

All present enzymatic activity of Crystal Structure of Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Methotrexate, Fdump and 4-((2-Amino-6-Methyl-4-Oxo-4,7- Dihydro-3H-Pyrrolo[2,3-D]Pyrimidin-5-Yl)Thio)-2-Chlorophenyl)-L- Glutamic Acid:
1.5.1.3; 2.1.1.45;

Protein crystallography data

The structure of Crystal Structure of Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Methotrexate, Fdump and 4-((2-Amino-6-Methyl-4-Oxo-4,7- Dihydro-3H-Pyrrolo[2,3-D]Pyrimidin-5-Yl)Thio)-2-Chlorophenyl)-L- Glutamic Acid, PDB code: 4ky8 was solved by V.P.Kumar, K.S.Anderson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.12 / 3.08
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 214.162, 115.665, 218.767, 90.00, 94.36, 90.00
R / Rfree (%) 23.2 / 26.6

Other elements in 4ky8:

The structure of Crystal Structure of Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Methotrexate, Fdump and 4-((2-Amino-6-Methyl-4-Oxo-4,7- Dihydro-3H-Pyrrolo[2,3-D]Pyrimidin-5-Yl)Thio)-2-Chlorophenyl)-L- Glutamic Acid also contains other interesting chemical elements:

Chlorine (Cl) 5 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Methotrexate, Fdump and 4-((2-Amino-6-Methyl-4-Oxo-4,7- Dihydro-3H-Pyrrolo[2,3-D]Pyrimidin-5-Yl)Thio)-2-Chlorophenyl)-L- Glutamic Acid (pdb code 4ky8). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 5 binding sites of Fluorine where determined in the Crystal Structure of Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Methotrexate, Fdump and 4-((2-Amino-6-Methyl-4-Oxo-4,7- Dihydro-3H-Pyrrolo[2,3-D]Pyrimidin-5-Yl)Thio)-2-Chlorophenyl)-L- Glutamic Acid, PDB code: 4ky8:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5;

Fluorine binding site 1 out of 5 in 4ky8

Go back to Fluorine Binding Sites List in 4ky8
Fluorine binding site 1 out of 5 in the Crystal Structure of Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Methotrexate, Fdump and 4-((2-Amino-6-Methyl-4-Oxo-4,7- Dihydro-3H-Pyrrolo[2,3-D]Pyrimidin-5-Yl)Thio)-2-Chlorophenyl)-L- Glutamic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Methotrexate, Fdump and 4-((2-Amino-6-Methyl-4-Oxo-4,7- Dihydro-3H-Pyrrolo[2,3-D]Pyrimidin-5-Yl)Thio)-2-Chlorophenyl)-L- Glutamic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F602

b:0.5
occ:1.00
 F5 A:UFP602 0.0 0.5 1.0
C5 A:UFP602 1.4 88.4 1.0
C6 A:UFP602 2.3 80.7 1.0
C4 A:UFP602 2.4 87.2 1.0
O4 A:UFP602 2.7 84.1 1.0
N1 A:UFP602 3.6 80.3 1.0
N3 A:UFP602 3.6 84.4 1.0
CAX A:1UF604 3.7 82.9 1.0
CAA A:1UF604 3.7 78.2 1.0
CBB A:1UF604 3.8 81.0 1.0
OH A:TYR342 3.9 0.4 1.0
SAS A:1UF604 4.0 85.2 1.0
C2 A:UFP602 4.1 82.5 1.0
CZ2 A:TRP316 4.2 63.4 1.0
SG A:CYS402 4.3 85.2 1.0
CH2 A:TRP316 4.3 60.7 1.0
NAR A:1UF604 4.4 89.2 1.0
CB A:CYS402 4.4 73.3 1.0
CE2 A:TYR342 4.5 0.4 1.0
CBE A:1UF604 4.5 81.8 1.0
CD2 A:LEU399 4.6 66.9 1.0
CZ A:TYR342 4.6 0.3 1.0
O4' A:UFP602 4.7 79.3 1.0
C1' A:UFP602 4.8 80.7 1.0
CD2 A:HIS403 4.8 80.2 1.0
CBD A:1UF604 4.9 82.7 1.0
NE2 A:HIS403 4.9 83.3 1.0

Fluorine binding site 2 out of 5 in 4ky8

Go back to Fluorine Binding Sites List in 4ky8
Fluorine binding site 2 out of 5 in the Crystal Structure of Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Methotrexate, Fdump and 4-((2-Amino-6-Methyl-4-Oxo-4,7- Dihydro-3H-Pyrrolo[2,3-D]Pyrimidin-5-Yl)Thio)-2-Chlorophenyl)-L- Glutamic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Methotrexate, Fdump and 4-((2-Amino-6-Methyl-4-Oxo-4,7- Dihydro-3H-Pyrrolo[2,3-D]Pyrimidin-5-Yl)Thio)-2-Chlorophenyl)-L- Glutamic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F602

b:0.9
occ:1.00
 F5 B:UFP602 0.0 0.9 1.0
C5 B:UFP602 1.4 91.8 1.0
C6 B:UFP602 2.3 84.2 1.0
C4 B:UFP602 2.4 90.6 1.0
O4 B:UFP602 2.7 87.5 1.0
N1 B:UFP602 3.6 83.8 1.0
N3 B:UFP602 3.6 87.8 1.0
CAA B:1UF604 3.7 87.6 1.0
CAX B:1UF604 3.7 92.2 1.0
OH B:TYR342 3.8 86.9 1.0
CBB B:1UF604 3.8 90.3 1.0
SAS B:1UF604 3.8 94.5 1.0
C2 B:UFP602 4.1 86.0 1.0
SG B:CYS402 4.2 0.1 1.0
CB B:CYS402 4.3 88.3 1.0
CE2 B:TYR342 4.4 83.9 1.0
CZ2 B:TRP316 4.4 94.5 1.0
CZ B:TYR342 4.5 85.8 1.0
CH2 B:TRP316 4.5 91.8 1.0
NAR B:1UF604 4.5 98.5 1.0
CD2 B:HIS403 4.6 76.2 1.0
CBE B:1UF604 4.6 91.2 1.0
CD2 B:LEU399 4.7 71.0 1.0
NE2 B:HIS403 4.7 79.4 1.0
O4' B:UFP602 4.7 82.8 1.0
C1' B:UFP602 4.8 84.2 1.0

Fluorine binding site 3 out of 5 in 4ky8

Go back to Fluorine Binding Sites List in 4ky8
Fluorine binding site 3 out of 5 in the Crystal Structure of Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Methotrexate, Fdump and 4-((2-Amino-6-Methyl-4-Oxo-4,7- Dihydro-3H-Pyrrolo[2,3-D]Pyrimidin-5-Yl)Thio)-2-Chlorophenyl)-L- Glutamic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Methotrexate, Fdump and 4-((2-Amino-6-Methyl-4-Oxo-4,7- Dihydro-3H-Pyrrolo[2,3-D]Pyrimidin-5-Yl)Thio)-2-Chlorophenyl)-L- Glutamic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F602

b:0.4
occ:1.00
 F5 C:UFP602 0.0 0.4 1.0
C5 C:UFP602 1.4 91.3 1.0
C6 C:UFP602 2.3 83.7 1.0
C4 C:UFP602 2.4 90.1 1.0
O4 C:UFP602 2.7 87.0 1.0
CBB C:1UF604 3.6 88.4 1.0
N1 C:UFP602 3.6 83.3 1.0
SAS C:1UF604 3.6 92.6 1.0
N3 C:UFP602 3.6 87.4 1.0
CAX C:1UF604 3.7 90.3 1.0
CAA C:1UF604 3.7 85.6 1.0
OH C:TYR342 4.1 1.0 1.0
C2 C:UFP602 4.1 85.5 1.0
CZ2 C:TRP316 4.2 66.3 1.0
SG C:CYS402 4.3 0.7 1.0
CH2 C:TRP316 4.4 63.6 1.0
CBE C:1UF604 4.4 89.2 1.0
CB C:CYS402 4.5 0.9 1.0
NAR C:1UF604 4.5 96.6 1.0
CE2 C:TYR342 4.6 0.0 1.0
CD2 C:LEU399 4.6 0.5 1.0
CZ C:TYR342 4.7 0.9 1.0
O4' C:UFP602 4.7 82.3 1.0
C1' C:UFP602 4.8 83.7 1.0
CBD C:1UF604 4.9 90.1 1.0
CD2 C:HIS403 4.9 98.6 1.0

Fluorine binding site 4 out of 5 in 4ky8

Go back to Fluorine Binding Sites List in 4ky8
Fluorine binding site 4 out of 5 in the Crystal Structure of Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Methotrexate, Fdump and 4-((2-Amino-6-Methyl-4-Oxo-4,7- Dihydro-3H-Pyrrolo[2,3-D]Pyrimidin-5-Yl)Thio)-2-Chlorophenyl)-L- Glutamic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Methotrexate, Fdump and 4-((2-Amino-6-Methyl-4-Oxo-4,7- Dihydro-3H-Pyrrolo[2,3-D]Pyrimidin-5-Yl)Thio)-2-Chlorophenyl)-L- Glutamic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F602

b:0.4
occ:1.00
 F5 D:UFP602 0.0 0.4 1.0
C5 D:UFP602 1.4 0.3 1.0
C6 D:UFP602 2.3 95.7 1.0
C4 D:UFP602 2.4 0.1 1.0
O4 D:UFP602 2.7 99.0 1.0
N1 D:UFP602 3.6 95.3 1.0
N3 D:UFP602 3.6 99.3 1.0
OH D:TYR342 3.9 98.5 1.0
CBB D:1UF604 4.0 0.6 1.0
CAX D:1UF604 4.0 0.5 1.0
C2 D:UFP602 4.1 97.5 1.0
CAA D:1UF604 4.1 0.8 1.0
SAS D:1UF604 4.1 0.8 1.0
SG D:CYS402 4.3 0.1 1.0
CZ2 D:TRP316 4.3 0.4 1.0
CB D:CYS402 4.3 99.2 1.0
CE2 D:TYR342 4.4 95.5 1.0
CH2 D:TRP316 4.4 0.7 1.0
CZ D:TYR342 4.5 97.5 1.0
CD2 D:HIS403 4.5 93.0 1.0
NE2 D:HIS403 4.6 96.2 1.0
CBE D:1UF604 4.7 0.4 1.0
NAR D:1UF604 4.7 0.8 1.0
O4' D:UFP602 4.7 94.3 1.0
CD2 D:LEU399 4.8 0.0 1.0
C1' D:UFP602 4.8 95.7 1.0

Fluorine binding site 5 out of 5 in 4ky8

Go back to Fluorine Binding Sites List in 4ky8
Fluorine binding site 5 out of 5 in the Crystal Structure of Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Methotrexate, Fdump and 4-((2-Amino-6-Methyl-4-Oxo-4,7- Dihydro-3H-Pyrrolo[2,3-D]Pyrimidin-5-Yl)Thio)-2-Chlorophenyl)-L- Glutamic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Methotrexate, Fdump and 4-((2-Amino-6-Methyl-4-Oxo-4,7- Dihydro-3H-Pyrrolo[2,3-D]Pyrimidin-5-Yl)Thio)-2-Chlorophenyl)-L- Glutamic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F602

b:0.9
occ:1.00
 F5 E:UFP602 0.0 0.9 1.0
C5 E:UFP602 1.4 0.8 1.0
C6 E:UFP602 2.3 0.2 1.0
C4 E:UFP602 2.4 0.6 1.0
O4 E:UFP602 2.7 0.5 1.0
N1 E:UFP602 3.6 0.8 1.0
N3 E:UFP602 3.6 0.8 1.0
SAS E:1UF604 4.0 0.1 1.0
CBB E:1UF604 4.0 0.9 1.0
CAA E:1UF604 4.1 0.1 1.0
CAX E:1UF604 4.1 0.8 1.0
C2 E:UFP602 4.1 1.0 1.0
OH E:TYR342 4.1 0.3 1.0
SG E:CYS402 4.2 0.7 1.0
CB E:CYS402 4.3 0.8 1.0
CZ2 E:TRP316 4.4 0.4 1.0
CH2 E:TRP316 4.6 0.7 1.0
CD2 E:LEU399 4.7 0.9 1.0
O4' E:UFP602 4.7 0.8 1.0
CE2 E:TYR342 4.8 0.3 1.0
CBE E:1UF604 4.8 0.7 1.0
C1' E:UFP602 4.8 0.2 1.0
CZ E:TYR342 4.8 0.2 1.0
CD2 E:HIS403 4.8 0.2 1.0
NAR E:1UF604 4.8 0.1 1.0

Reference:

V.P.Kumar, K.M.Frey, Y.Wang, H.K.Jain, A.Gangjee, K.S.Anderson. Substituted Pyrrolo[2,3-D]Pyrimidines As Cryptosporidium Hominis Thymidylate Synthase Inhibitors. Bioorg.Med.Chem.Lett. V. 23 5426 2013.
ISSN: ISSN 0960-894X
PubMed: 23927969
DOI: 10.1016/J.BMCL.2013.07.037
Page generated: Mon Jul 14 22:55:24 2025

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy