Atomistry » Fluorine » PDB 6pf9-6q0j » 6pf9
Atomistry »
  Fluorine »
    PDB 6pf9-6q0j »
      6pf9 »

Fluorine in PDB 6pf9: Crystal Structure of Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Fdump and 2-(2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H- Pyrrolo[2,3-D]Pyrimidin-5-Yl)Methyl)Benzamido)Phenyl)Acetic Acid.

Protein crystallography data

The structure of Crystal Structure of Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Fdump and 2-(2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H- Pyrrolo[2,3-D]Pyrimidin-5-Yl)Methyl)Benzamido)Phenyl)Acetic Acid., PDB code: 6pf9 was solved by D.J.Czyzyk, M.Valhondo, W.L.Jorgensen, K.S.Anderson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.59 / 2.89
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 214.201, 116.510, 221.439, 90.00, 94.87, 90.00
R / Rfree (%) 21.3 / 24.2

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Fdump and 2-(2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H- Pyrrolo[2,3-D]Pyrimidin-5-Yl)Methyl)Benzamido)Phenyl)Acetic Acid. (pdb code 6pf9). 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, Fdump and 2-(2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H- Pyrrolo[2,3-D]Pyrimidin-5-Yl)Methyl)Benzamido)Phenyl)Acetic Acid., PDB code: 6pf9:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5;

Fluorine binding site 1 out of 5 in 6pf9

Go back to Fluorine Binding Sites List in 6pf9
Fluorine binding site 1 out of 5 in the Crystal Structure of Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Fdump and 2-(2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H- Pyrrolo[2,3-D]Pyrimidin-5-Yl)Methyl)Benzamido)Phenyl)Acetic 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, Fdump and 2-(2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H- Pyrrolo[2,3-D]Pyrimidin-5-Yl)Methyl)Benzamido)Phenyl)Acetic Acid. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F602

b:0.9
occ:1.00
F5 A:UFP602 0.0 0.9 1.0
C5 A:UFP602 1.4 0.2 1.0
C6 A:UFP602 2.3 0.9 1.0
C4 A:UFP602 2.4 0.3 1.0
O4 A:UFP602 2.7 0.9 1.0
C6 A:OF7603 3.4 0.8 1.0
C5 A:OF7603 3.5 0.0 1.0
N1 A:UFP602 3.6 0.7 1.0
N3 A:UFP602 3.6 0.4 1.0
OH A:TYR342 3.7 0.8 1.0
C7 A:OF7603 3.9 0.9 1.0
N3 A:OF7603 3.9 0.5 1.0
SG A:CYS402 4.0 0.3 1.0
C2 A:OF7603 4.1 0.2 1.0
C2 A:UFP602 4.1 0.4 1.0
CH2 A:TRP316 4.2 0.5 1.0
CZ2 A:TRP316 4.2 0.6 1.0
C1 A:OF7603 4.3 0.7 1.0
CB A:CYS402 4.3 84.9 1.0
CD2 A:LEU399 4.4 0.3 1.0
CZ A:TYR342 4.5 0.1 1.0
CE2 A:TYR342 4.5 0.4 1.0
O4' A:UFP602 4.6 0.6 1.0
C1' A:UFP602 4.7 0.4 1.0

Fluorine binding site 2 out of 5 in 6pf9

Go back to Fluorine Binding Sites List in 6pf9
Fluorine binding site 2 out of 5 in the Crystal Structure of Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Fdump and 2-(2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H- Pyrrolo[2,3-D]Pyrimidin-5-Yl)Methyl)Benzamido)Phenyl)Acetic 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, Fdump and 2-(2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H- Pyrrolo[2,3-D]Pyrimidin-5-Yl)Methyl)Benzamido)Phenyl)Acetic Acid. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F602

b:0.3
occ:1.00
F5 B:UFP602 0.0 0.3 1.0
C5 B:UFP602 1.4 0.7 1.0
C6 B:UFP602 2.3 0.5 1.0
C4 B:UFP602 2.4 0.7 1.0
O4 B:UFP602 2.7 0.5 1.0
C6 B:OF7603 3.2 0.4 1.0
C5 B:OF7603 3.4 0.2 1.0
N3 B:OF7603 3.6 0.1 1.0
N1 B:UFP602 3.6 0.2 1.0
N3 B:UFP602 3.6 0.1 1.0
C7 B:OF7603 3.9 96.0 1.0
C2 B:OF7603 3.9 0.3 1.0
C1 B:OF7603 4.0 0.3 1.0
CZ2 B:TRP316 4.1 0.1 1.0
CH2 B:TRP316 4.1 0.2 1.0
C2 B:UFP602 4.1 98.9 1.0
OH B:TYR342 4.1 96.9 1.0
SG B:CYS402 4.2 92.8 1.0
CB B:CYS402 4.5 75.9 1.0
CD2 B:LEU399 4.5 0.9 1.0
O4' B:UFP602 4.6 0.3 1.0
CE2 B:TYR342 4.7 87.7 1.0
C1' B:UFP602 4.7 0.4 1.0
CZ B:TYR342 4.8 83.5 1.0
C3 B:OF7603 4.9 0.5 1.0
N1 B:OF7603 5.0 0.2 1.0
CZ3 B:TRP316 5.0 0.4 1.0
CE2 B:TRP316 5.0 0.9 1.0

Fluorine binding site 3 out of 5 in 6pf9

Go back to Fluorine Binding Sites List in 6pf9
Fluorine binding site 3 out of 5 in the Crystal Structure of Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Fdump and 2-(2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H- Pyrrolo[2,3-D]Pyrimidin-5-Yl)Methyl)Benzamido)Phenyl)Acetic 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, Fdump and 2-(2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H- Pyrrolo[2,3-D]Pyrimidin-5-Yl)Methyl)Benzamido)Phenyl)Acetic Acid. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F602

b:87.7
occ:1.00
F5 C:UFP602 0.0 87.7 1.0
C5 C:UFP602 1.4 92.8 1.0
C6 C:UFP602 2.3 88.6 1.0
C4 C:UFP602 2.4 96.0 1.0
O4 C:UFP602 2.7 87.5 1.0
C6 C:OF7603 3.2 94.8 1.0
C5 C:OF7603 3.2 85.6 1.0
C7 C:OF7603 3.6 87.6 1.0
N1 C:UFP602 3.6 85.4 1.0
N3 C:UFP602 3.6 99.7 1.0
N3 C:OF7603 3.8 99.3 1.0
C2 C:OF7603 3.8 98.8 1.0
OH C:TYR342 4.0 92.2 1.0
SG C:CYS402 4.0 91.0 1.0
C2 C:UFP602 4.1 87.7 1.0
C1 C:OF7603 4.1 81.0 1.0
CH2 C:TRP316 4.2 79.3 1.0
CZ2 C:TRP316 4.2 73.4 1.0
CD2 C:LEU399 4.3 65.2 1.0
CB C:CYS402 4.5 68.5 1.0
O4' C:UFP602 4.6 86.2 1.0
CE2 C:TYR342 4.7 77.0 1.0
C3 C:OF7603 4.7 0.5 1.0
C1' C:UFP602 4.7 88.0 1.0
CZ C:TYR342 4.7 80.6 1.0

Fluorine binding site 4 out of 5 in 6pf9

Go back to Fluorine Binding Sites List in 6pf9
Fluorine binding site 4 out of 5 in the Crystal Structure of Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Fdump and 2-(2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H- Pyrrolo[2,3-D]Pyrimidin-5-Yl)Methyl)Benzamido)Phenyl)Acetic 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, Fdump and 2-(2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H- Pyrrolo[2,3-D]Pyrimidin-5-Yl)Methyl)Benzamido)Phenyl)Acetic Acid. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F602

b:99.0
occ:1.00
F5 D:UFP602 0.0 99.0 1.0
C5 D:UFP602 1.4 94.7 1.0
C6 D:UFP602 2.3 92.5 1.0
C4 D:UFP602 2.4 98.0 1.0
O4 D:UFP602 2.7 98.8 1.0
C6 D:OF7603 3.1 87.7 1.0
C5 D:OF7603 3.3 83.3 1.0
N1 D:UFP602 3.6 93.7 1.0
N3 D:UFP602 3.6 94.6 1.0
N3 D:OF7603 3.7 0.2 1.0
C7 D:OF7603 3.7 75.7 1.0
CH2 D:TRP316 3.9 60.3 1.0
CZ2 D:TRP316 3.9 82.2 1.0
C2 D:OF7603 3.9 0.3 1.0
OH D:TYR342 4.0 85.7 1.0
C1 D:OF7603 4.1 96.5 1.0
C2 D:UFP602 4.1 94.0 1.0
SG D:CYS402 4.2 87.7 1.0
CD2 D:LEU399 4.5 81.2 1.0
CB D:CYS402 4.5 74.4 1.0
CE2 D:TYR342 4.6 76.3 1.0
O4' D:UFP602 4.6 83.1 1.0
CZ D:TYR342 4.7 73.3 1.0
C1' D:UFP602 4.7 81.7 1.0
CZ3 D:TRP316 4.8 67.9 1.0
CE2 D:TRP316 4.8 82.0 1.0
C3 D:OF7603 4.9 94.1 1.0

Fluorine binding site 5 out of 5 in 6pf9

Go back to Fluorine Binding Sites List in 6pf9
Fluorine binding site 5 out of 5 in the Crystal Structure of Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Fdump and 2-(2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H- Pyrrolo[2,3-D]Pyrimidin-5-Yl)Methyl)Benzamido)Phenyl)Acetic 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, Fdump and 2-(2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H- Pyrrolo[2,3-D]Pyrimidin-5-Yl)Methyl)Benzamido)Phenyl)Acetic Acid. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F602

b:0.8
occ:1.00
F5 E:UFP602 0.0 0.8 1.0
C5 E:UFP602 1.4 0.5 1.0
C6 E:UFP602 2.3 1.0 1.0
C4 E:UFP602 2.4 0.0 1.0
O4 E:UFP602 2.7 0.7 1.0
C6 E:OF7603 3.4 0.1 1.0
C5 E:OF7603 3.4 0.8 1.0
N1 E:UFP602 3.6 0.7 1.0
N3 E:UFP602 3.6 0.8 1.0
C7 E:OF7603 3.6 0.4 1.0
OH E:TYR342 3.8 96.2 1.0
N3 E:OF7603 4.0 0.5 1.0
C2 E:OF7603 4.0 0.5 1.0
C2 E:UFP602 4.1 0.9 1.0
SG E:CYS402 4.2 92.2 1.0
CZ2 E:TRP316 4.2 0.8 1.0
CH2 E:TRP316 4.2 92.4 1.0
C1 E:OF7603 4.3 0.7 1.0
CB E:CYS402 4.4 76.7 1.0
CE2 E:TYR342 4.5 87.4 1.0
CZ E:TYR342 4.5 86.7 1.0
O4' E:UFP602 4.7 97.6 1.0
CD2 E:LEU399 4.7 0.4 1.0
C1' E:UFP602 4.8 87.2 1.0
CD2 E:HIS403 4.9 85.8 1.0
C3 E:OF7603 4.9 0.5 1.0
NE2 E:HIS403 5.0 92.8 1.0

Reference:

D.J.Czyzyk, M.Valhondo, L.Deiana, J.Tirado-Rives, W.L.Jorgensen, K.S.Anderson. Structure Activity Relationship Towards Design of Cryptosporidium Specific Thymidylate Synthase Inhibitors. Eur.J.Med.Chem. V. 183 11673 2019.
ISSN: ISSN 0223-5234
PubMed: 31536894
DOI: 10.1016/J.EJMECH.2019.111673
Page generated: Fri Aug 2 00:22:34 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy