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Fluorine in PDB 7t0c: Cryptococcus Neoformans Protein Farnesyltransferase in Complex with Fpp and Inhibitor 2E

Enzymatic activity of Cryptococcus Neoformans Protein Farnesyltransferase in Complex with Fpp and Inhibitor 2E

All present enzymatic activity of Cryptococcus Neoformans Protein Farnesyltransferase in Complex with Fpp and Inhibitor 2E:
2.5.1.58;

Protein crystallography data

The structure of Cryptococcus Neoformans Protein Farnesyltransferase in Complex with Fpp and Inhibitor 2E, PDB code: 7t0c was solved by Y.Wang, Y.Shi, L.S.Beese, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 70.96 / 1.90
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 141.915, 141.915, 130.226, 90, 90, 90
R / Rfree (%) 17.9 / 20.1

Other elements in 7t0c:

The structure of Cryptococcus Neoformans Protein Farnesyltransferase in Complex with Fpp and Inhibitor 2E also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Zinc (Zn) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Cryptococcus Neoformans Protein Farnesyltransferase in Complex with Fpp and Inhibitor 2E (pdb code 7t0c). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Cryptococcus Neoformans Protein Farnesyltransferase in Complex with Fpp and Inhibitor 2E, PDB code: 7t0c:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 7t0c

Go back to Fluorine Binding Sites List in 7t0c
Fluorine binding site 1 out of 6 in the Cryptococcus Neoformans Protein Farnesyltransferase in Complex with Fpp and Inhibitor 2E


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Cryptococcus Neoformans Protein Farnesyltransferase in Complex with Fpp and Inhibitor 2E within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F602

b:39.7
occ:0.59
 F15 B:XN4602 0.0 39.7 0.6
C14 B:XN4602 1.4 37.5 0.6
F17 B:XN4602 2.2 36.8 0.6
F16 B:XN4602 2.2 41.4 0.6
O13 B:XN4602 2.3 34.1 0.6
O1 B:EDO629 2.6 43.9 1.0
C18 B:XN4602 2.7 38.5 0.4
C12 B:XN4602 2.8 34.4 0.6
C12 B:XN4602 2.8 37.1 0.4
C08 B:XN4602 2.9 35.9 0.4
C18 B:XN4602 3.0 37.3 0.6
CZ2 B:TRP94 3.0 33.9 1.0
C11 B:XN4602 3.1 34.6 0.4
CD1 B:TYR409 3.2 32.6 1.0
CE1 B:TYR409 3.2 34.9 1.0
C09 B:XN4602 3.2 37.5 0.4
C10 B:XN4602 3.3 37.8 0.4
O13 B:XN4602 3.5 38.6 0.4
C1 B:EDO629 3.6 43.9 1.0
CE2 B:TRP94 3.7 31.6 1.0
NE1 B:TRP94 3.7 31.4 1.0
N07 B:XN4602 3.7 35.8 0.4
C06 B:XN4602 3.8 34.6 0.4
C11 B:XN4602 3.8 35.6 0.6
CH2 B:TRP94 4.0 31.9 1.0
C08 B:XN4602 4.1 37.3 0.6
CE3 B:TRP90 4.4 31.4 1.0
CG B:TYR409 4.4 30.9 1.0
CZ2 B:TRP329 4.4 36.0 1.0
CZ B:TYR409 4.4 31.1 1.0
CZ3 B:TRP90 4.5 30.1 1.0
C04 B:XN4602 4.7 35.3 0.4
CD2 B:TRP90 4.7 30.4 1.0
ND2 B:ASN413 4.7 34.8 1.0
C06 B:XN4602 4.8 35.1 0.6
C10 B:XN4602 4.8 35.1 0.6
C05 B:XN4602 4.8 35.1 0.4
C14 B:XN4602 4.8 34.0 0.4
C14 B:FPP643 4.9 32.1 0.6
N07 B:XN4602 4.9 35.2 0.6
C09 B:XN4602 4.9 36.3 0.6
C2 B:EDO629 4.9 33.9 1.0
CH2 B:TRP90 5.0 28.6 1.0

Fluorine binding site 2 out of 6 in 7t0c

Go back to Fluorine Binding Sites List in 7t0c
Fluorine binding site 2 out of 6 in the Cryptococcus Neoformans Protein Farnesyltransferase in Complex with Fpp and Inhibitor 2E


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Cryptococcus Neoformans Protein Farnesyltransferase in Complex with Fpp and Inhibitor 2E within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F602

b:32.5
occ:0.41
 F15 B:XN4602 0.0 32.5 0.4
C15 B:FPP643 1.2 30.3 0.6
C14 B:XN4602 1.4 34.0 0.4
C13 B:FPP643 2.1 32.6 0.6
F16 B:XN4602 2.2 33.4 0.4
O13 B:XN4602 2.2 38.6 0.4
F17 B:XN4602 2.3 34.1 0.4
C14 B:FPP643 2.9 32.1 0.6
C12 B:FPP643 3.0 34.7 0.6
F17 B:XN4602 3.4 36.8 0.6
C12 B:XN4602 3.6 37.1 0.4
CH2 B:TRP329 3.6 34.1 1.0
CH2 B:TRP90 3.7 28.6 1.0
CE2 B:TYR200 4.0 26.4 1.0
CD2 B:TYR200 4.1 25.1 1.0
CZ3 B:TRP329 4.1 28.3 1.0
C11 B:XN4602 4.3 34.6 0.4
SG B:CYS201 4.3 28.3 1.0
C11 B:FPP643 4.4 36.3 0.6
CZ2 B:TRP90 4.4 29.3 1.0
CZ3 B:TRP90 4.5 30.1 1.0
C14 B:XN4602 4.6 37.5 0.6
C18 B:XN4602 4.6 38.5 0.4
SG B:CYS272 4.6 29.8 1.0
CZ2 B:TRP329 4.7 36.0 1.0
F16 B:XN4602 4.7 41.4 0.6
O B:HOH859 4.8 30.7 1.0
C1 B:EDO629 4.8 43.9 1.0
CE2 B:TYR144 4.9 30.3 1.0
O B:HOH763 4.9 26.3 1.0
O B:HOH709 5.0 34.9 1.0

Fluorine binding site 3 out of 6 in 7t0c

Go back to Fluorine Binding Sites List in 7t0c
Fluorine binding site 3 out of 6 in the Cryptococcus Neoformans Protein Farnesyltransferase in Complex with Fpp and Inhibitor 2E


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Cryptococcus Neoformans Protein Farnesyltransferase in Complex with Fpp and Inhibitor 2E within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F602

b:41.4
occ:0.59
 F16 B:XN4602 0.0 41.4 0.6
C18 B:XN4602 0.5 38.5 0.4
C14 B:XN4602 1.4 37.5 0.6
C08 B:XN4602 1.5 35.9 0.4
C12 B:XN4602 1.6 37.1 0.4
F15 B:XN4602 2.2 39.7 0.6
F17 B:XN4602 2.3 36.8 0.6
O13 B:XN4602 2.3 34.1 0.6
N07 B:XN4602 2.5 35.8 0.4
C09 B:XN4602 2.5 37.5 0.4
O13 B:XN4602 2.5 38.6 0.4
C11 B:XN4602 2.6 34.6 0.4
C10 B:XN4602 2.9 37.8 0.4
C18 B:XN4602 3.0 37.3 0.6
C12 B:XN4602 3.0 34.4 0.6
C06 B:XN4602 3.0 34.6 0.4
C14 B:FPP643 3.2 32.1 0.6
CL34 B:XN4602 3.4 35.2 0.6
C11 B:FPP643 3.6 36.3 0.6
C14 B:XN4602 3.6 34.0 0.4
F16 B:XN4602 3.6 33.4 0.4
C35 B:XN4602 3.7 34.5 0.6
C19 B:XN4602 3.8 35.8 0.4
C9 B:FPP643 3.8 34.5 0.6
CZ2 B:TRP329 3.9 36.0 1.0
C13 B:FPP643 3.9 32.6 0.6
C12 B:FPP643 4.0 34.7 0.6
C33 B:XN4602 4.0 35.8 0.6
CE1 B:TYR409 4.1 34.9 1.0
F17 B:XN4602 4.2 34.1 0.4
O1 B:EDO629 4.2 43.9 1.0
O20 B:XN4602 4.2 38.5 0.4
C08 B:XN4602 4.3 37.3 0.6
CH2 B:TRP329 4.3 34.1 1.0
C11 B:XN4602 4.3 35.6 0.6
C05 B:XN4602 4.4 35.1 0.4
C8 B:FPP643 4.4 33.5 0.6
C35 B:XN4602 4.7 34.9 0.4
F15 B:XN4602 4.7 32.5 0.4
CL34 B:XN4602 4.7 35.8 0.4
CD1 B:TYR409 4.7 32.6 1.0
C04 B:XN4602 4.8 35.3 0.4
C1 B:EDO629 4.8 43.9 1.0
C33 B:XN4602 4.8 34.9 0.4
CE2 B:TRP329 4.8 31.9 1.0
CZ B:TYR409 4.9 31.1 1.0
C36 B:XN4602 4.9 32.5 0.6
OH B:TYR409 4.9 30.2 1.0
N07 B:XN4602 4.9 35.2 0.6
C21 B:XN4602 5.0 36.2 0.4

Fluorine binding site 4 out of 6 in 7t0c

Go back to Fluorine Binding Sites List in 7t0c
Fluorine binding site 4 out of 6 in the Cryptococcus Neoformans Protein Farnesyltransferase in Complex with Fpp and Inhibitor 2E


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Cryptococcus Neoformans Protein Farnesyltransferase in Complex with Fpp and Inhibitor 2E within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F602

b:33.4
occ:0.41
 F16 B:XN4602 0.0 33.4 0.4
C13 B:FPP643 0.6 32.6 0.6
C12 B:FPP643 0.9 34.7 0.6
C14 B:XN4602 1.4 34.0 0.4
C15 B:FPP643 1.8 30.3 0.6
C14 B:FPP643 1.8 32.1 0.6
C11 B:FPP643 2.2 36.3 0.6
F15 B:XN4602 2.2 32.5 0.4
F17 B:XN4602 2.2 34.1 0.4
O13 B:XN4602 2.3 38.6 0.4
C12 B:XN4602 3.0 37.1 0.4
C9 B:FPP643 3.1 34.5 0.6
CH2 B:TRP329 3.4 34.1 1.0
C18 B:XN4602 3.4 38.5 0.4
F17 B:XN4602 3.6 36.8 0.6
CL34 B:XN4602 3.6 35.8 0.4
F16 B:XN4602 3.6 41.4 0.6
SG B:CYS272 3.8 29.8 1.0
CZ3 B:TRP329 3.9 28.3 1.0
CG B:ARG197 4.0 35.2 1.0
CZ2 B:TRP329 4.1 36.0 1.0
C11 B:XN4602 4.1 34.6 0.4
C14 B:XN4602 4.2 37.5 0.6
CD B:ARG197 4.5 34.5 1.0
C8 B:FPP643 4.5 33.5 0.6
CB B:ARG197 4.6 31.0 1.0
C08 B:XN4602 4.6 35.9 0.4
O13 B:XN4602 4.8 34.1 0.6
CE3 B:TRP329 4.9 26.0 1.0

Fluorine binding site 5 out of 6 in 7t0c

Go back to Fluorine Binding Sites List in 7t0c
Fluorine binding site 5 out of 6 in the Cryptococcus Neoformans Protein Farnesyltransferase in Complex with Fpp and Inhibitor 2E


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Cryptococcus Neoformans Protein Farnesyltransferase in Complex with Fpp and Inhibitor 2E within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F602

b:36.8
occ:0.59
 F17 B:XN4602 0.0 36.8 0.6
C14 B:XN4602 1.4 37.5 0.6
O13 B:XN4602 1.4 38.6 0.4
C12 B:XN4602 1.5 37.1 0.4
C11 B:XN4602 2.1 34.6 0.4
F15 B:XN4602 2.2 39.7 0.6
F16 B:XN4602 2.3 41.4 0.6
O13 B:XN4602 2.3 34.1 0.6
C18 B:XN4602 2.4 38.5 0.4
C14 B:XN4602 2.8 34.0 0.4
O1 B:EDO629 3.0 43.9 1.0
C10 B:XN4602 3.2 37.8 0.4
C14 B:FPP643 3.2 32.1 0.6
C1 B:EDO629 3.2 43.9 1.0
CZ3 B:TRP90 3.3 30.1 1.0
CH2 B:TRP90 3.3 28.6 1.0
F15 B:XN4602 3.4 32.5 0.4
C08 B:XN4602 3.4 35.9 0.4
F17 B:XN4602 3.5 34.1 0.4
C12 B:XN4602 3.6 34.4 0.6
F16 B:XN4602 3.6 33.4 0.4
C13 B:FPP643 3.7 32.6 0.6
C09 B:XN4602 3.7 37.5 0.4
CE3 B:TRP90 3.7 31.4 1.0
CZ2 B:TRP90 3.8 29.3 1.0
CH2 B:TRP329 4.0 34.1 1.0
CZ2 B:TRP329 4.0 36.0 1.0
CE2 B:TRP90 4.2 30.8 1.0
CD2 B:TRP90 4.2 30.4 1.0
C15 B:FPP643 4.2 30.3 0.6
C18 B:XN4602 4.3 37.3 0.6
C12 B:FPP643 4.4 34.7 0.6
C11 B:XN4602 4.6 35.6 0.6
CZ2 B:TRP94 4.6 33.9 1.0
N07 B:XN4602 4.6 35.8 0.4
NE1 B:TRP94 4.7 31.4 1.0
C11 B:FPP643 4.7 36.3 0.6
C2 B:EDO629 4.7 33.9 1.0
CE1 B:TYR409 4.9 34.9 1.0

Fluorine binding site 6 out of 6 in 7t0c

Go back to Fluorine Binding Sites List in 7t0c
Fluorine binding site 6 out of 6 in the Cryptococcus Neoformans Protein Farnesyltransferase in Complex with Fpp and Inhibitor 2E


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Cryptococcus Neoformans Protein Farnesyltransferase in Complex with Fpp and Inhibitor 2E within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F602

b:34.1
occ:0.41
 F17 B:XN4602 0.0 34.1 0.4
C14 B:FPP643 1.2 32.1 0.6
C14 B:XN4602 1.4 34.0 0.4
C13 B:FPP643 1.7 32.6 0.6
C15 B:FPP643 2.0 30.3 0.6
F16 B:XN4602 2.2 33.4 0.4
F15 B:XN4602 2.3 32.5 0.4
O13 B:XN4602 2.3 38.6 0.4
C12 B:XN4602 2.8 37.1 0.4
C12 B:FPP643 3.0 34.7 0.6
C11 B:XN4602 3.1 34.6 0.4
F17 B:XN4602 3.5 36.8 0.6
CG B:LEU141 3.7 30.6 1.0
CD2 B:LEU141 3.7 29.9 1.0
CZ2 B:TRP90 3.8 29.3 1.0
C18 B:XN4602 3.9 38.5 0.4
C11 B:FPP643 3.9 36.3 0.6
CH2 B:TRP90 3.9 28.6 1.0
SG B:CYS201 4.0 28.3 1.0
CB B:ARG197 4.1 31.0 1.0
F16 B:XN4602 4.2 41.4 0.6
C14 B:XN4602 4.2 37.5 0.6
O13 B:XN4602 4.2 34.1 0.6
CG B:ARG197 4.2 35.2 1.0
C10 B:XN4602 4.2 37.8 0.4
CD B:ARG197 4.5 34.5 1.0
CD1 B:LEU141 4.5 26.6 1.0
CB B:LEU141 4.8 28.6 1.0
CA B:ARG197 4.8 28.6 1.0
C08 B:XN4602 4.8 35.9 0.4
O B:ARG197 4.8 27.8 1.0
CE2 B:TRP90 4.9 30.8 1.0
C09 B:XN4602 5.0 37.5 0.4
CZ3 B:TRP90 5.0 30.1 1.0

Reference:

Y.Wang, F.Xu, C.B.Nichols, Y.Shi, H.W.Hellinga, J.A.Alspaugh, M.D.Distefano, L.S.Beese. Structure-Guided Discovery of Potent Antifungals That Prevent Ras Signaling By Inhibiting Protein Farnesyltransferase. J.Med.Chem. V. 65 13753 2022.
ISSN: ISSN 0022-2623
PubMed: 36218371
DOI: 10.1021/ACS.JMEDCHEM.2C00902
Page generated: Wed Jul 16 00:19:41 2025

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