Fluorine in PDB 7c04: Crystal Structure of Human TRAP1 with DN203492

The structure of Crystal Structure of Human TRAP1 with DN203492, PDB code: 7c04 was solved by D.Kim, D.Kim, S.Y.Kim, J.H.Lee, B.H.Kang, S.Kang, C.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.21 / 1.70
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	110.405, 110.405, 59.445, 90.00, 90.00, 120.00
R / Rfree (%)	18.9 / 23.4

The structure of Crystal Structure of Human TRAP1 with DN203492 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Fluorine atom in the Crystal Structure of Human TRAP1 with DN203492 (pdb code 7c04). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of Human TRAP1 with DN203492, PDB code: 7c04:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of Human TRAP1 with DN203492


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 Human TRAP1 with DN203492 within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:32.3 occ:1.00 F20 A:FEU301 0.0 32.3 1.0 C19 A:FEU301 1.3 37.6 1.0 F21 A:FEU301 2.2 32.7 1.0 F22 A:FEU301 2.2 39.8 1.0 C16 A:FEU301 2.3 24.9 1.0 H1 A:FEU301 2.8 32.7 1.0 C15 A:FEU301 2.9 27.3 1.0 CD1 A:LEU172 3.3 37.8 1.0 CZ2 A:TRP231 3.3 26.7 1.0 C17 A:FEU301 3.4 22.4 1.0 CB A:LEU172 3.5 37.9 1.0 CE2 A:PHE205 3.5 31.5 1.0 H2 A:FEU301 3.7 26.9 1.0 CE2 A:TRP231 3.8 22.9 1.0 CG A:LEU172 3.8 45.6 1.0 O A:HOH479 3.8 40.0 1.0 CH2 A:TRP231 3.9 27.0 1.0 CD2 A:PHE205 3.9 29.6 1.0 CA A:LEU172 4.0 42.7 1.0 NE1 A:TRP231 4.1 29.3 1.0 N A:LEU172 4.1 38.2 1.0 C14 A:FEU301 4.3 23.7 1.0 CD2 A:LEU172 4.4 48.8 1.0 CZ A:PHE205 4.4 25.7 1.0 C18 A:FEU301 4.6 21.3 1.0 CD2 A:TRP231 4.6 24.2 1.0 CZ3 A:TRP231 4.7 27.8 1.0 O A:LEU168 4.8 28.3 1.0 H11 A:FEU301 4.9 28.4 1.0 C13 A:FEU301 5.0 23.2 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of Human TRAP1 with DN203492


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 Human TRAP1 with DN203492 within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:32.7 occ:1.00 F21 A:FEU301 0.0 32.7 1.0 C19 A:FEU301 1.3 37.6 1.0 F20 A:FEU301 2.2 32.3 1.0 F22 A:FEU301 2.2 39.8 1.0 H2 A:FEU301 2.3 26.9 1.0 C16 A:FEU301 2.3 24.9 1.0 C17 A:FEU301 2.7 22.4 1.0 CE2 A:TRP231 3.1 22.9 1.0 NE1 A:TRP231 3.4 29.3 1.0 CD2 A:TRP231 3.5 24.2 1.0 CZ2 A:TRP231 3.5 26.7 1.0 C15 A:FEU301 3.6 27.3 1.0 CD1 A:TRP231 3.8 25.3 1.0 CE2 A:PHE205 3.9 31.5 1.0 CG A:TRP231 3.9 23.3 1.0 H1 A:FEU301 4.0 32.7 1.0 CH2 A:TRP231 4.0 27.0 1.0 CD2 A:LEU168 4.0 26.7 1.0 CE3 A:TRP231 4.0 22.3 1.0 C18 A:FEU301 4.1 21.3 1.0 H5 A:FEU301 4.1 33.2 1.0 CZ A:PHE205 4.1 25.7 1.0 CZ3 A:TRP231 4.3 27.8 1.0 O A:LEU168 4.5 28.3 1.0 CD2 A:PHE205 4.6 29.6 1.0 C14 A:FEU301 4.8 23.7 1.0 C24 A:FEU301 4.8 27.6 1.0 CG2 A:VAL217 4.8 22.7 1.0 CE A:MET163 4.8 26.3 1.0 H3 A:FEU301 4.8 33.2 1.0 CA A:LEU168 4.9 23.1 1.0 CB A:TRP231 4.9 22.8 1.0 O A:HOH479 4.9 40.0 1.0 C13 A:FEU301 4.9 23.2 1.0 O23 A:FEU301 5.0 22.9 1.0 CE1 A:PHE205 5.0 23.2 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of Human TRAP1 with DN203492


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 Human TRAP1 with DN203492 within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:39.8 occ:1.00 F22 A:FEU301 0.0 39.8 1.0 C19 A:FEU301 1.3 37.6 1.0 F21 A:FEU301 2.2 32.7 1.0 F20 A:FEU301 2.2 32.3 1.0 C16 A:FEU301 2.3 24.9 1.0 H1 A:FEU301 2.9 32.7 1.0 C15 A:FEU301 2.9 27.3 1.0 O A:HOH479 3.3 40.0 1.0 C17 A:FEU301 3.3 22.4 1.0 O A:LEU168 3.4 28.3 1.0 H2 A:FEU301 3.6 26.9 1.0 O A:GLU167 3.6 29.0 1.0 CA A:LEU168 3.7 23.1 1.0 C A:LEU168 3.8 30.2 1.0 NE1 A:TRP231 3.9 29.3 1.0 CE A:MET163 4.0 26.3 1.0 N A:LEU172 4.0 38.2 1.0 CB A:ASN171 4.1 28.7 1.0 CE2 A:TRP231 4.2 22.9 1.0 C14 A:FEU301 4.2 23.7 1.0 CD2 A:LEU168 4.3 26.7 1.0 CB A:LEU172 4.4 37.9 1.0 CZ2 A:TRP231 4.4 26.7 1.0 C A:GLU167 4.5 27.6 1.0 C18 A:FEU301 4.5 21.3 1.0 CD1 A:TRP231 4.5 25.3 1.0 N A:LEU168 4.6 24.6 1.0 N A:ASN171 4.6 36.5 1.0 CA A:LEU172 4.6 42.7 1.0 C A:ASN171 4.6 35.0 1.0 CA A:ASN171 4.7 34.6 1.0 CB A:LEU168 4.7 23.8 1.0 C13 A:FEU301 4.9 23.2 1.0 H11 A:FEU301 4.9 28.4 1.0 SD A:MET163 4.9 24.9 1.0 N A:VAL169 5.0 31.7 1.0

D.Kim, S.Y.Kim, D.Kim, N.G.Yoon, J.Yun, K.B.Hong, C.Lee, J.H.Lee, B.H.Kang, S.Kang. Development of Pyrazolo[3,4-D]Pyrimidine-6-Amine-Based TRAP1 Inhibitors That Demonstrate in Vivo Anticancer Activity in Mouse Xenograft Models. Bioorg.Chem. V. 101 03901 2020.
ISSN: ISSN 0045-2068
PubMed: 32590225
DOI: 10.1016/J.BIOORG.2020.103901