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Fluorine in PDB 4kfo: Structure-Based Discovery of Novel Amide-Containing Nicotinamide Phosphoribosyltransferase (Nampt) Inhibitors

Enzymatic activity of Structure-Based Discovery of Novel Amide-Containing Nicotinamide Phosphoribosyltransferase (Nampt) Inhibitors

All present enzymatic activity of Structure-Based Discovery of Novel Amide-Containing Nicotinamide Phosphoribosyltransferase (Nampt) Inhibitors:
2.4.2.12;

Protein crystallography data

The structure of Structure-Based Discovery of Novel Amide-Containing Nicotinamide Phosphoribosyltransferase (Nampt) Inhibitors, PDB code: 4kfo was solved by X.Zheng, P.Bauer, T.Baumeister, A.J.Buckmelter, M.Caligiuri, K.H.Clodfelter, B.Han, Y.Ho, N.Kley, J.Lin, D.J.Reynolds, G.Sharma, C.C.Smith, Z.Wang, P.S.Dragovich, J.Gunzner-Tosteb, B.M.Liederer, J.Ly, T.O'brien, A.Oh, L.Wang, W.Wang, Y.Xiao, M.Zak, G.Zhao, P.Yuen, K.W.Bair, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.91 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 60.779, 106.439, 82.917, 90.00, 96.55, 90.00
R / Rfree (%) 15.5 / 18.1

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure-Based Discovery of Novel Amide-Containing Nicotinamide Phosphoribosyltransferase (Nampt) Inhibitors (pdb code 4kfo). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Structure-Based Discovery of Novel Amide-Containing Nicotinamide Phosphoribosyltransferase (Nampt) Inhibitors, PDB code: 4kfo:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 4kfo

Go back to Fluorine Binding Sites List in 4kfo
Fluorine binding site 1 out of 4 in the Structure-Based Discovery of Novel Amide-Containing Nicotinamide Phosphoribosyltransferase (Nampt) Inhibitors


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure-Based Discovery of Novel Amide-Containing Nicotinamide Phosphoribosyltransferase (Nampt) Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:23.9
occ:1.00
 F29 A:1QS601 0.0 23.9 1.0
C27 A:1QS601 1.4 23.0 1.0
C26 A:1QS601 2.4 22.8 1.0
C28 A:1QS601 2.4 20.1 1.0
CD1 A:TYR188 3.4 17.7 1.0
O A:TYR240 3.6 14.0 1.0
CE1 A:TYR188 3.6 20.9 1.0
C25 A:1QS601 3.6 24.9 1.0
C23 A:1QS601 3.7 21.4 1.0
C A:TYR240 3.9 15.1 1.0
CA A:SER241 4.0 14.3 1.0
O A:HOH1042 4.1 42.8 1.0
C24 A:1QS601 4.1 24.7 1.0
N A:SER241 4.1 11.7 1.0
CE1 A:HIS191 4.2 12.4 1.0
O A:HOH729 4.2 16.0 1.0
CB A:TYR240 4.3 11.4 1.0
C A:SER241 4.4 13.9 1.0
ND1 A:HIS191 4.4 13.2 1.0
CA A:GLY217 4.5 12.1 1.0
CG A:TYR188 4.5 16.6 1.0
CG1 A:VAL242 4.6 16.6 1.0
F30 A:1QS601 4.7 30.5 1.0
CA A:TYR240 4.7 14.2 1.0
N A:VAL242 4.8 12.8 1.0
O A:SER241 4.8 13.7 1.0
CZ A:TYR188 4.8 22.6 1.0

Fluorine binding site 2 out of 4 in 4kfo

Go back to Fluorine Binding Sites List in 4kfo
Fluorine binding site 2 out of 4 in the Structure-Based Discovery of Novel Amide-Containing Nicotinamide Phosphoribosyltransferase (Nampt) Inhibitors


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure-Based Discovery of Novel Amide-Containing Nicotinamide Phosphoribosyltransferase (Nampt) Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:30.5
occ:1.00
 F30 A:1QS601 0.0 30.5 1.0
C25 A:1QS601 1.3 24.9 1.0
C26 A:1QS601 2.4 22.8 1.0
C24 A:1QS601 2.4 24.7 1.0
O A:HOH971 3.3 40.0 1.0
C27 A:1QS601 3.6 23.0 1.0
C23 A:1QS601 3.6 21.4 1.0
CG A:PRO273 3.6 18.6 1.0
CB A:PRO273 3.8 16.6 1.0
O A:HOH1181 3.8 40.6 1.0
O A:HOH1131 4.1 42.7 1.0
C28 A:1QS601 4.1 20.1 1.0
CG1 A:VAL242 4.1 16.6 1.0
O A:HOH1231 4.3 52.9 1.0
CG2 A:VAL242 4.5 17.4 1.0
O A:HOH1042 4.5 42.8 1.0
CD1 A:ILE309 4.7 20.5 1.0
F29 A:1QS601 4.7 23.9 1.0
CB A:VAL242 4.9 14.9 1.0

Fluorine binding site 3 out of 4 in 4kfo

Go back to Fluorine Binding Sites List in 4kfo
Fluorine binding site 3 out of 4 in the Structure-Based Discovery of Novel Amide-Containing Nicotinamide Phosphoribosyltransferase (Nampt) Inhibitors


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure-Based Discovery of Novel Amide-Containing Nicotinamide Phosphoribosyltransferase (Nampt) Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F601

b:25.1
occ:1.00
 F29 B:1QS601 0.0 25.1 1.0
C27 B:1QS601 1.4 28.5 1.0
C26 B:1QS601 2.4 27.2 1.0
C28 B:1QS601 2.4 22.1 1.0
CD1 B:TYR188 3.4 13.8 1.0
C25 B:1QS601 3.6 32.1 1.0
C23 B:1QS601 3.6 20.7 1.0
CE1 B:TYR188 3.6 18.3 1.0
O B:TYR240 3.7 13.0 1.0
O B:HOH1205 3.8 49.0 1.0
C B:TYR240 4.0 9.9 1.0
CA B:SER241 4.0 11.7 1.0
C24 B:1QS601 4.1 26.4 1.0
O B:HOH729 4.1 14.7 1.0
N B:SER241 4.2 11.2 1.0
CE1 B:HIS191 4.2 10.1 1.0
CB B:TYR240 4.3 9.6 1.0
C B:SER241 4.3 11.7 1.0
ND1 B:HIS191 4.4 10.9 1.0
CG1 B:VAL242 4.5 17.0 1.0
CG B:TYR188 4.5 15.0 1.0
CA B:GLY217 4.6 12.9 1.0
O B:SER241 4.7 14.7 1.0
F30 B:1QS601 4.7 28.5 1.0
CA B:TYR240 4.8 12.8 1.0
N B:VAL242 4.8 11.5 1.0
CZ B:TYR188 4.8 20.5 1.0

Fluorine binding site 4 out of 4 in 4kfo

Go back to Fluorine Binding Sites List in 4kfo
Fluorine binding site 4 out of 4 in the Structure-Based Discovery of Novel Amide-Containing Nicotinamide Phosphoribosyltransferase (Nampt) Inhibitors


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure-Based Discovery of Novel Amide-Containing Nicotinamide Phosphoribosyltransferase (Nampt) Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F601

b:28.5
occ:1.00
 F30 B:1QS601 0.0 28.5 1.0
C25 B:1QS601 1.3 32.1 1.0
C26 B:1QS601 2.4 27.2 1.0
C24 B:1QS601 2.4 26.4 1.0
O B:HOH1008 3.4 44.6 1.0
O B:HOH1085 3.6 48.6 1.0
C23 B:1QS601 3.6 20.7 1.0
C27 B:1QS601 3.6 28.5 1.0
CG B:PRO273 3.7 14.4 1.0
CB B:PRO273 3.8 15.9 1.0
CG1 B:VAL242 4.1 17.0 1.0
C28 B:1QS601 4.1 22.1 1.0
O B:HOH1000 4.3 48.4 1.0
CD1 B:ILE309 4.6 18.2 1.0
CG2 B:VAL242 4.6 18.3 1.0
O B:HOH1205 4.6 49.0 1.0
F29 B:1QS601 4.7 25.1 1.0
CB B:VAL242 4.9 17.1 1.0
O B:HOH995 4.9 26.9 1.0

Reference:

X.Zheng, P.Bauer, T.Baumeister, A.J.Buckmelter, M.Caligiuri, K.H.Clodfelter, B.Han, Y.C.Ho, N.Kley, J.Lin, D.J.Reynolds, G.Sharma, C.C.Smith, Z.Wang, P.S.Dragovich, A.Oh, W.Wang, M.Zak, J.Gunzner-Toste, G.Zhao, P.W.Yuen, K.W.Bair. Structure-Based Identification of Ureas As Novel Nicotinamide Phosphoribosyltransferase (Nampt) Inhibitors. J.Med.Chem. V. 56 4921 2013.
ISSN: ISSN 0022-2623
PubMed: 23617784
DOI: 10.1021/JM400186H
Page generated: Thu Aug 1 03:12:41 2024

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