Fluorine in PDB 5tbm: Crystal Structure of PT2385 Bound to HIF2A-B*:Arnt-B* Complex

The structure of Crystal Structure of PT2385 Bound to HIF2A-B*:Arnt-B* Complex, PDB code: 5tbm was solved by X.Du, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.89 / 1.85
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	73.400, 84.097, 41.401, 90.00, 106.24, 90.00
R / Rfree (%)	23.8 / 30

The binding sites of Fluorine atom in the Crystal Structure of PT2385 Bound to HIF2A-B*:Arnt-B* Complex (pdb code 5tbm). 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 PT2385 Bound to HIF2A-B*:Arnt-B* Complex, PDB code: 5tbm:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of PT2385 Bound to HIF2A-B*:Arnt-B* Complex


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 PT2385 Bound to HIF2A-B*:Arnt-B* Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:33.9 occ:1.00 F1 A:79A401 0.0 33.9 1.0 C10 A:79A401 1.4 32.3 1.0 C5 A:79A401 2.4 35.2 1.0 C9 A:79A401 2.4 28.9 1.0 CE2 A:PHE244 3.2 33.4 1.0 CZ A:PHE244 3.3 32.8 1.0 ND2 A:ASN341 3.3 29.0 1.0 CG A:ASN341 3.4 28.9 1.0 OD1 A:ASN341 3.6 33.7 1.0 C6 A:79A401 3.6 32.4 1.0 C8 A:79A401 3.7 28.6 1.0 OG A:SER246 3.8 28.9 1.0 CB A:ASN341 4.0 30.5 1.0 C7 A:79A401 4.2 32.2 1.0 CZ A:PHE254 4.2 29.6 1.0 CE2 A:PHE254 4.2 33.0 1.0 CD1 A:LEU319 4.4 38.6 1.0 CD2 A:PHE244 4.4 32.6 1.0 CB A:SER246 4.5 27.8 1.0 OH A:TYR307 4.5 37.4 1.0 CE1 A:PHE244 4.6 32.9 1.0 C17 A:79A401 4.7 37.6 1.0 CD1 A:ILE261 4.8 28.7 1.0 SD A:MET309 4.8 40.2 1.0 O1 A:79A401 4.8 27.7 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of PT2385 Bound to HIF2A-B*:Arnt-B* Complex


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 PT2385 Bound to HIF2A-B*:Arnt-B* Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:39.3 occ:1.00 F3 A:79A401 0.0 39.3 1.0 C11 A:79A401 1.3 39.6 1.0 F2 A:79A401 2.1 36.9 1.0 C15 A:79A401 2.3 30.8 1.0 C12 A:79A401 2.5 31.9 1.0 O4 A:79A401 2.7 37.6 1.0 CE1 A:HIS293 3.4 49.2 1.0 ND1 A:HIS293 3.4 39.1 1.0 CD1 A:ILE337 3.4 28.5 1.0 C14 A:79A401 3.5 28.7 1.0 CG A:MET252 3.5 63.0 1.0 C13 A:79A401 3.6 32.1 1.0 CA A:MET252 3.6 48.4 1.0 CB A:MET252 3.8 51.4 1.0 CB A:HIS248 4.2 29.8 1.0 N A:MET252 4.3 50.8 1.0 CG2 A:ILE337 4.4 26.7 1.0 O A:SER249 4.4 35.7 1.0 CG A:HIS248 4.5 29.8 1.0 CB A:ILE337 4.5 30.8 1.0 CG1 A:ILE337 4.5 30.1 1.0 SD A:MET252 4.6 79.4 1.0 C A:MET252 4.7 40.0 1.0 NE2 A:HIS293 4.7 45.2 1.0 CG A:HIS293 4.7 44.4 1.0 O A:MET252 4.8 39.0 1.0 C1 A:79A401 4.8 28.3 1.0 O A:HOH502 4.8 50.8 1.0 ND1 A:HIS248 4.8 29.6 1.0 CD2 A:LEU296 4.9 43.3 1.0 C4 A:79A401 4.9 33.6 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of PT2385 Bound to HIF2A-B*:Arnt-B* Complex


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 PT2385 Bound to HIF2A-B*:Arnt-B* Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:36.9 occ:1.00 F2 A:79A401 0.0 36.9 1.0 C11 A:79A401 1.3 39.6 1.0 F3 A:79A401 2.1 39.3 1.0 C15 A:79A401 2.3 30.8 1.0 C12 A:79A401 2.3 31.9 1.0 CG2 A:ILE337 2.8 26.7 1.0 C14 A:79A401 3.0 28.7 1.0 C13 A:79A401 3.0 32.1 1.0 CB A:ILE337 3.4 30.8 1.0 SG A:CYS339 3.4 32.8 1.0 O4 A:79A401 3.5 37.6 1.0 CD1 A:ILE337 3.7 28.5 1.0 CG A:HIS248 3.7 29.8 1.0 CB A:HIS248 3.7 29.8 1.0 CD2 A:HIS248 3.8 29.6 1.0 CG1 A:ILE337 4.1 30.1 1.0 C1 A:79A401 4.1 28.3 1.0 C4 A:79A401 4.2 33.6 1.0 O2 A:79A401 4.4 35.9 1.0 ND1 A:HIS248 4.4 29.6 1.0 CD2 A:LEU296 4.5 43.3 1.0 O1 A:79A401 4.5 27.7 1.0 NE2 A:HIS248 4.6 29.4 1.0 CA A:ILE337 4.7 26.3 1.0 CE1 A:HIS248 4.9 24.6 1.0 O A:ILE337 4.9 27.6 1.0 C A:ILE337 4.9 30.3 1.0 ND1 A:HIS293 4.9 39.1 1.0

E.M.Wallace, J.P.Rizzi, G.Han, P.M.Wehn, Z.Cao, X.Du, T.Cheng, R.M.Czerwinski, D.D.Dixon, B.S.Goggin, J.A.Grina, M.M.Halfmann, M.A.Maddie, S.R.Olive, S.T.Schlachter, H.Tan, B.Wang, K.Wang, S.Xie, R.Xu, H.Yang, J.A.Josey. A Small-Molecule Antagonist of HIF2 Alpha Is Efficacious in Preclinical Models of Renal Cell Carcinoma. Cancer Res. V. 76 5491 2016.
ISSN: ESSN 1538-7445
PubMed: 27635045
DOI: 10.1158/0008-5472.CAN-16-0473