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Bromine in PDB 7t0d: Cryptococcus Neoformans Protein Farnesyltransferase in Complex with Fpp and Inhibitor 2K

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

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

Protein crystallography data

The structure of Cryptococcus Neoformans Protein Farnesyltransferase in Complex with Fpp and Inhibitor 2K, PDB code: 7t0d 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) 42.43 / 1.91
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 (%) 17.3 / 19.5

Other elements in 7t0d:

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

Zinc (Zn) 1 atom
Fluorine (F) 6 atoms

Bromine Binding Sites:

The binding sites of Bromine atom in the Cryptococcus Neoformans Protein Farnesyltransferase in Complex with Fpp and Inhibitor 2K (pdb code 7t0d). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 2 binding sites of Bromine where determined in the Cryptococcus Neoformans Protein Farnesyltransferase in Complex with Fpp and Inhibitor 2K, PDB code: 7t0d:
Jump to Bromine binding site number: 1; 2;

Bromine binding site 1 out of 2 in 7t0d

Go back to Bromine Binding Sites List in 7t0d
Bromine binding site 1 out of 2 in the Cryptococcus Neoformans Protein Farnesyltransferase in Complex with Fpp and Inhibitor 2K


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Cryptococcus Neoformans Protein Farnesyltransferase in Complex with Fpp and Inhibitor 2K within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br602

b:47.4
occ:0.42
BR33 B:XO7602 0.0 47.4 0.4
O19 B:XO7602 1.0 42.6 0.6
C18 B:XO7602 1.6 38.1 0.6
C32 B:XO7602 1.9 38.1 0.4
N06 B:XO7602 2.1 37.6 0.6
C07 B:XO7602 2.3 39.6 0.6
C17 B:XO7602 2.6 38.5 0.6
C31 B:XO7602 2.9 39.1 0.4
C34 B:XO7602 2.9 37.9 0.4
C20 B:XO7602 3.1 36.5 0.6
C08 B:XO7602 3.2 39.0 0.6
F15 B:XO7602 3.2 39.4 0.4
OH A:TYR109 3.5 48.9 1.0
C05 B:XO7602 3.5 35.8 0.6
C11 B:XO7602 3.6 38.5 0.6
C17 B:XO7602 3.7 38.2 0.4
C11 B:FPP646 3.8 40.6 0.4
CE2 A:TYR109 3.8 47.4 1.0
NH1 B:ARG197 3.9 39.2 1.0
C7 B:FPP646 3.9 38.1 0.4
C31 B:XO7602 3.9 39.9 0.6
N21 B:XO7602 4.0 38.0 0.6
CD B:ARG197 4.0 34.4 1.0
CZ A:TYR109 4.0 49.4 1.0
C09 B:XO7602 4.1 37.6 0.6
C32 B:XO7602 4.1 37.4 0.6
C30 B:XO7602 4.2 38.3 0.4
C8 B:FPP646 4.2 38.6 0.4
C35 B:XO7602 4.2 36.6 0.4
C07 B:XO7602 4.2 38.4 0.4
C04 B:XO7602 4.2 36.0 0.6
C10 B:XO7602 4.3 38.1 0.6
C11 B:XO7602 4.3 36.2 0.4
C6 B:FPP646 4.4 38.9 0.4
C13 B:XO7602 4.4 38.0 0.4
N06 B:XO7602 4.4 35.8 0.4
C30 B:XO7602 4.4 38.5 0.6
O19 B:XO7602 4.5 39.5 0.4
C14 B:FPP646 4.5 37.1 0.4
O12 B:XO7602 4.5 36.7 0.4
C18 B:XO7602 4.5 39.4 0.4
O12 B:XO7602 4.5 37.5 0.6
C9 B:FPP646 4.6 38.9 0.4
BR33 B:XO7602 4.6 45.9 0.6
C03 B:XO7602 4.7 36.1 0.6
C29 B:XO7602 4.7 37.6 0.4
C34 B:XO7602 4.7 36.2 0.6
CZ B:ARG197 4.8 40.9 1.0
NE B:ARG197 4.8 38.8 1.0
C5 B:FPP646 4.9 38.7 0.4
C10 B:FPP646 4.9 35.8 0.4
CD2 A:TYR109 4.9 49.8 1.0
C29 B:XO7602 5.0 37.4 0.6

Bromine binding site 2 out of 2 in 7t0d

Go back to Bromine Binding Sites List in 7t0d
Bromine binding site 2 out of 2 in the Cryptococcus Neoformans Protein Farnesyltransferase in Complex with Fpp and Inhibitor 2K


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Cryptococcus Neoformans Protein Farnesyltransferase in Complex with Fpp and Inhibitor 2K within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br602

b:45.9
occ:0.58
BR33 B:XO7602 0.0 45.9 0.6
C9 B:FPP646 0.6 38.9 0.4
C8 B:FPP646 1.6 38.6 0.4
C11 B:FPP646 1.8 40.6 0.4
C32 B:XO7602 2.0 37.4 0.6
C7 B:FPP646 2.2 38.1 0.4
C12 B:FPP646 2.8 35.8 0.4
C10 B:FPP646 2.9 35.8 0.4
C31 B:XO7602 2.9 39.9 0.6
C34 B:XO7602 3.0 36.2 0.6
CA B:GLY268 3.5 29.7 1.0
C B:GLY268 3.6 30.6 1.0
C6 B:FPP646 3.7 38.9 0.4
O12 B:XO7602 3.7 37.5 0.6
O B:GLY268 3.7 25.7 1.0
C17 B:XO7602 3.8 38.5 0.6
CG B:ARG197 3.9 35.3 1.0
C13 B:FPP646 4.0 36.8 0.4
N B:TYR269 4.2 25.5 1.0
CD B:ARG197 4.2 34.4 1.0
C11 B:XO7602 4.2 38.5 0.6
C30 B:XO7602 4.3 38.5 0.6
C35 B:XO7602 4.3 36.4 0.6
CE1 B:TYR269 4.3 33.9 1.0
SG B:CYS272 4.4 31.4 1.0
CD1 B:TYR269 4.4 32.9 1.0
C5 B:FPP646 4.5 38.7 0.4
BR33 B:XO7602 4.6 47.4 0.4
C14 B:FPP646 4.6 37.1 0.4
F15 B:XO7602 4.6 40.8 0.6
CZ2 B:TRP329 4.7 37.8 1.0
CH2 B:TRP329 4.7 36.4 1.0
N B:GLY268 4.8 27.0 1.0
C13 B:XO7602 4.8 37.2 0.6
CE2 B:TRP329 4.8 35.4 1.0
F15 B:XO7602 4.8 39.4 0.4
C29 B:XO7602 4.8 37.4 0.6
CZ B:TYR269 4.8 40.3 1.0
C34 B:XO7602 4.9 37.9 0.4
CZ3 B:TRP329 4.9 31.5 1.0
C07 B:XO7602 4.9 39.6 0.6
CA B:TYR269 4.9 25.8 1.0
C32 B:XO7602 4.9 38.1 0.4
CD2 B:TRP329 5.0 27.1 1.0
CG B:TYR269 5.0 26.3 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: Thu Jul 11 04:35:18 2024

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