Fluorine in PDB 6zxo: Crystal Structure of His-Tagged Human Thymidylate Synthase (Ht-Hts) in Complex with Fdump and Raltitrexed (Tomudex)

Enzymatic activity of Crystal Structure of His-Tagged Human Thymidylate Synthase (Ht-Hts) in Complex with Fdump and Raltitrexed (Tomudex)

All present enzymatic activity of Crystal Structure of His-Tagged Human Thymidylate Synthase (Ht-Hts) in Complex with Fdump and Raltitrexed (Tomudex):
2.1.1.45;

Protein crystallography data

The structure of Crystal Structure of His-Tagged Human Thymidylate Synthase (Ht-Hts) in Complex with Fdump and Raltitrexed (Tomudex), PDB code: 6zxo was solved by C.Pozzi, S.Mangani, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.33 / 2.60
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 61.72, 95.87, 103.84, 112.39, 91.47, 109.17
R / Rfree (%) 17.2 / 23.2

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of His-Tagged Human Thymidylate Synthase (Ht-Hts) in Complex with Fdump and Raltitrexed (Tomudex) (pdb code 6zxo). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of His-Tagged Human Thymidylate Synthase (Ht-Hts) in Complex with Fdump and Raltitrexed (Tomudex), PDB code: 6zxo:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 6zxo

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Fluorine binding site 1 out of 6 in the Crystal Structure of His-Tagged Human Thymidylate Synthase (Ht-Hts) in Complex with Fdump and Raltitrexed (Tomudex)


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 His-Tagged Human Thymidylate Synthase (Ht-Hts) in Complex with Fdump and Raltitrexed (Tomudex) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F402

b:61.4
occ:1.00
 F5 A:UFP402 0.0 61.4 1.0
C5 A:UFP402 1.4 49.4 1.0
C6 A:UFP402 2.4 47.7 1.0
C4 A:UFP402 2.4 47.2 1.0
O4 A:UFP402 2.8 50.0 1.0
CH2 A:TRP109 3.4 45.1 1.0
C6 A:D16401 3.6 48.1 1.0
N3 A:UFP402 3.6 41.6 1.0
N1 A:UFP402 3.6 39.5 1.0
CZ2 A:TRP109 3.7 43.4 1.0
C7 A:D16401 3.8 49.4 1.0
C9 A:D16401 3.8 49.2 1.0
C5 A:D16401 3.9 42.1 1.0
C2 A:UFP402 4.1 39.4 1.0
CD2 A:LEU192 4.1 73.9 1.0
SG A:CYS195 4.2 81.3 1.0
CP1 A:D16401 4.2 57.3 1.0
C8 A:D16401 4.3 45.1 1.0
C4A A:D16401 4.5 40.7 1.0
N10 A:D16401 4.5 55.2 1.0
OH A:TYR135 4.6 62.4 1.0
CZ3 A:TRP109 4.6 46.3 1.0
C8A A:D16401 4.7 41.2 1.0
CB A:CYS195 4.8 67.2 1.0
C1' A:UFP402 4.9 35.1 1.0
O4' A:UFP402 4.9 37.4 1.0

Fluorine binding site 2 out of 6 in 6zxo

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Fluorine binding site 2 out of 6 in the Crystal Structure of His-Tagged Human Thymidylate Synthase (Ht-Hts) in Complex with Fdump and Raltitrexed (Tomudex)


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 His-Tagged Human Thymidylate Synthase (Ht-Hts) in Complex with Fdump and Raltitrexed (Tomudex) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F402

b:77.5
occ:1.00
 F5 B:UFP402 0.0 77.5 1.0
C5 B:UFP402 1.3 52.6 1.0
C6 B:UFP402 2.3 47.7 1.0
C4 B:UFP402 2.4 51.0 1.0
O4 B:UFP402 2.8 51.7 1.0
N1 B:UFP402 3.5 45.0 1.0
N3 B:UFP402 3.6 48.8 1.0
CH2 B:TRP109 3.7 57.0 1.0
SG B:CYS195 3.7 94.2 1.0
C6 B:D16401 3.8 46.3 1.0
CZ2 B:TRP109 4.0 52.2 1.0
CD2 B:LEU192 4.0 57.3 1.0
C9 B:D16401 4.0 53.0 1.0
CP1 B:D16401 4.0 62.8 1.0
C7 B:D16401 4.0 47.0 1.0
C5 B:D16401 4.0 42.7 1.0
C2 B:UFP402 4.0 45.7 1.0
O B:HOH518 4.2 54.3 1.0
OH B:TYR135 4.3 58.8 1.0
N10 B:D16401 4.4 56.9 1.0
C4A B:D16401 4.5 46.9 1.0
C8 B:D16401 4.6 47.2 1.0
O4' B:UFP402 4.6 39.3 1.0
C1' B:UFP402 4.7 41.1 1.0
CZ3 B:TRP109 4.7 58.8 1.0
CB B:CYS195 4.7 68.3 1.0
C8A B:D16401 4.8 47.0 1.0

Fluorine binding site 3 out of 6 in 6zxo

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Fluorine binding site 3 out of 6 in the Crystal Structure of His-Tagged Human Thymidylate Synthase (Ht-Hts) in Complex with Fdump and Raltitrexed (Tomudex)


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 His-Tagged Human Thymidylate Synthase (Ht-Hts) in Complex with Fdump and Raltitrexed (Tomudex) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F402

b:58.3
occ:1.00
 F5 C:UFP402 0.0 58.3 1.0
C5 C:UFP402 1.3 41.9 1.0
C4 C:UFP402 2.4 42.1 1.0
C6 C:UFP402 2.4 39.3 1.0
O4 C:UFP402 2.6 40.4 1.0
SG C:CYS195 3.5 93.7 1.0
N3 C:UFP402 3.6 40.3 1.0
N1 C:UFP402 3.6 35.5 1.0
CH2 C:TRP109 3.7 73.4 1.0
CP1 C:D16401 3.8 52.8 1.0
CD2 C:LEU192 3.8 74.2 1.0
CB C:CYS195 3.8 67.6 1.0
OH C:TYR135 4.0 78.5 1.0
C2 C:UFP402 4.0 39.8 1.0
CZ2 C:TRP109 4.1 78.8 1.0
C6 C:D16401 4.3 37.2 1.0
NE2 C:HIS196 4.5 77.7 1.0
C5 C:D16401 4.5 33.3 1.0
C9 C:D16401 4.6 40.4 1.0
C7 C:D16401 4.6 35.3 1.0
N10 C:D16401 4.7 45.5 1.0
CZ3 C:TRP109 4.8 67.1 1.0
CE2 C:TYR135 4.8 70.7 1.0
C1' C:UFP402 4.9 34.9 1.0
CZ C:TYR135 4.9 71.0 1.0
O4' C:UFP402 4.9 38.5 1.0
C4A C:D16401 4.9 31.0 1.0
N C:CYS195 5.0 51.6 1.0

Fluorine binding site 4 out of 6 in 6zxo

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Fluorine binding site 4 out of 6 in the Crystal Structure of His-Tagged Human Thymidylate Synthase (Ht-Hts) in Complex with Fdump and Raltitrexed (Tomudex)


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 His-Tagged Human Thymidylate Synthase (Ht-Hts) in Complex with Fdump and Raltitrexed (Tomudex) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F402

b:54.2
occ:1.00
 F5 D:UFP402 0.0 54.2 1.0
C5 D:UFP402 1.4 45.1 1.0
C4 D:UFP402 2.4 46.6 1.0
C6 D:UFP402 2.4 42.9 1.0
O4 D:UFP402 2.7 49.6 1.0
CH2 D:TRP109 3.3 65.6 1.0
N3 D:UFP402 3.6 43.7 1.0
N1 D:UFP402 3.6 40.4 1.0
SG D:CYS195 3.7 99.9 1.0
C6 D:D16401 3.7 49.6 1.0
CZ2 D:TRP109 3.8 65.1 1.0
C9 D:D16401 3.8 51.1 1.0
CP1 D:D16401 3.9 49.9 1.0
C5 D:D16401 4.0 43.3 1.0
C7 D:D16401 4.1 48.5 1.0
C2 D:UFP402 4.1 40.6 1.0
O D:HOH534 4.2 46.9 1.0
N10 D:D16401 4.4 52.4 1.0
CD2 D:LEU192 4.5 67.9 1.0
CZ3 D:TRP109 4.5 69.1 1.0
OH D:TYR135 4.5 86.9 1.0
C4A D:D16401 4.6 39.9 1.0
C8 D:D16401 4.7 41.6 1.0
CB D:CYS195 4.8 99.9 1.0
O4' D:UFP402 4.9 41.1 1.0
C1' D:UFP402 4.9 37.9 1.0
C8A D:D16401 5.0 39.6 1.0

Fluorine binding site 5 out of 6 in 6zxo

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Fluorine binding site 5 out of 6 in the Crystal Structure of His-Tagged Human Thymidylate Synthase (Ht-Hts) in Complex with Fdump and Raltitrexed (Tomudex)


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 His-Tagged Human Thymidylate Synthase (Ht-Hts) in Complex with Fdump and Raltitrexed (Tomudex) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F402

b:64.9
occ:1.00
 F5 E:UFP402 0.0 64.9 1.0
C5 E:UFP402 1.4 49.9 1.0
C6 E:UFP402 2.4 44.1 1.0
C4 E:UFP402 2.5 46.5 1.0
O4 E:UFP402 2.8 46.9 1.0
CH2 E:TRP109 3.3 61.7 1.0
N1 E:UFP402 3.6 40.0 1.0
N3 E:UFP402 3.7 43.9 1.0
CD2 E:LEU192 3.7 61.7 1.0
CZ2 E:TRP109 3.8 57.8 1.0
CP1 E:D16401 3.9 56.4 1.0
C6 E:D16401 4.0 41.6 1.0
SG E:CYS195 4.0 76.7 1.0
C2 E:UFP402 4.1 40.9 1.0
CZ3 E:TRP109 4.1 64.6 1.0
C7 E:D16401 4.1 39.5 1.0
C5 E:D16401 4.2 40.4 1.0
OH E:TYR135 4.3 56.6 1.0
C9 E:D16401 4.4 50.1 1.0
C8 E:D16401 4.5 38.5 1.0
C4A E:D16401 4.5 42.0 1.0
O4' E:UFP402 4.6 31.3 1.0
N10 E:D16401 4.6 57.1 1.0
C8A E:D16401 4.6 38.7 1.0
C1' E:UFP402 4.7 34.8 1.0
CB E:CYS195 4.8 60.3 1.0
CG E:LEU192 5.0 58.4 1.0

Fluorine binding site 6 out of 6 in 6zxo

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Fluorine binding site 6 out of 6 in the Crystal Structure of His-Tagged Human Thymidylate Synthase (Ht-Hts) in Complex with Fdump and Raltitrexed (Tomudex)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of His-Tagged Human Thymidylate Synthase (Ht-Hts) in Complex with Fdump and Raltitrexed (Tomudex) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F402

b:68.2
occ:1.00
 F5 F:UFP402 0.0 68.2 1.0
C5 F:UFP402 1.3 51.1 1.0
C6 F:UFP402 2.4 44.5 1.0
C4 F:UFP402 2.4 46.6 1.0
O4 F:UFP402 2.7 49.5 1.0
N1 F:UFP402 3.6 40.1 1.0
N3 F:UFP402 3.6 40.5 1.0
CP1 F:D16401 3.8 71.6 1.0
SG F:CYS195 3.9 99.9 1.0
C6 F:D16401 3.9 55.9 1.0
OH F:TYR135 4.0 73.4 1.0
C2 F:UFP402 4.0 39.4 1.0
C9 F:D16401 4.2 58.3 1.0
C5 F:D16401 4.2 51.5 1.0
CH2 F:TRP109 4.2 67.0 1.0
C7 F:D16401 4.2 60.9 1.0
CB F:CYS195 4.4 76.6 1.0
N10 F:D16401 4.5 62.4 1.0
CZ2 F:TRP109 4.6 62.9 1.0
C4A F:D16401 4.7 47.1 1.0
C8 F:D16401 4.7 54.7 1.0
O4' F:UFP402 4.7 42.7 1.0
C1' F:UFP402 4.8 40.4 1.0
C8A F:D16401 4.9 48.8 1.0
CZ F:TYR135 5.0 82.0 1.0

Reference:

C.Pozzi, M.Santucci, G.Marverti, D.D'arca, L.Tagliazucchi, S.Ferrari, G.Gozzi, L.Losi, G.Tassone, S.Mangani, G.Ponterini, M.P.Costi. Structural Bases For the Synergistic Inhibition of Human Thymidylate Synthase and Ovarian Cancer Cell Growth By Drug Combinations. Cancers (Basel) V. 13 2021.
ISSN: ESSN 2072-6694
PubMed: 33923290
DOI: 10.3390/CANCERS13092061
Page generated: Sat Jul 10 14:00:42 2021

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