Fluorine in PDB 5ufp: Crystal Structure of PT2399 Bound to HIF2A-B*:Arnt-B* Complex

The structure of Crystal Structure of PT2399 Bound to HIF2A-B*:Arnt-B* Complex, PDB code: 5ufp 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 / 1.90
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	73.379, 84.057, 41.472, 90.00, 106.48, 90.00
R / Rfree (%)	21.8 / 27.1

The binding sites of Fluorine atom in the Crystal Structure of PT2399 Bound to HIF2A-B*:Arnt-B* Complex (pdb code 5ufp). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 5 binding sites of Fluorine where determined in the Crystal Structure of PT2399 Bound to HIF2A-B*:Arnt-B* Complex, PDB code: 5ufp:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5;

Fluorine binding site 1 out of 5 in the Crystal Structure of PT2399 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 PT2399 Bound to HIF2A-B*:Arnt-B* Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:30.3 occ:1.00 F1 A:86D401 0.0 30.3 1.0 C10 A:86D401 1.4 27.4 1.0 C5 A:86D401 2.4 28.8 1.0 C9 A:86D401 2.4 24.4 1.0 ND2 A:ASN341 3.1 26.6 1.0 CG A:ASN341 3.2 25.1 1.0 CE1 A:PHE244 3.3 25.4 1.0 CZ A:PHE244 3.4 28.4 1.0 OD1 A:ASN341 3.5 30.6 1.0 C6 A:86D401 3.7 26.9 1.0 C8 A:86D401 3.7 24.9 1.0 OG A:SER246 3.8 24.6 1.0 CB A:ASN341 3.9 26.5 1.0 C7 A:86D401 4.2 27.5 1.0 CD1 A:LEU319 4.2 32.7 1.0 CE1 A:PHE254 4.3 26.3 1.0 CZ A:PHE254 4.3 25.1 1.0 CB A:SER246 4.5 20.6 1.0 CD1 A:PHE244 4.5 25.7 1.0 OH A:TYR307 4.6 38.5 1.0 CE2 A:PHE244 4.7 24.7 1.0 C17 A:86D401 4.7 31.9 1.0 CD1 A:ILE261 4.7 26.5 1.0 SD A:MET309 4.8 31.9 1.0 O1 A:86D401 4.8 25.5 1.0

Fluorine binding site 2 out of 5 in the Crystal Structure of PT2399 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 PT2399 Bound to HIF2A-B*:Arnt-B* Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:31.8 occ:1.00 F5 A:86D401 0.0 31.8 1.0 C11 A:86D401 1.3 33.6 1.0 F2 A:86D401 2.2 32.4 1.0 C15 A:86D401 2.3 27.7 1.0 C12 A:86D401 2.4 32.3 1.0 O4 A:86D401 2.7 33.5 1.0 CE1 A:HIS293 3.4 51.0 1.0 CG A:MET252 3.5 54.9 1.0 C14 A:86D401 3.5 27.1 1.0 CD1 A:ILE337 3.5 26.7 1.0 CA A:MET252 3.5 41.0 1.0 ND1 A:HIS293 3.5 44.9 1.0 C13 A:86D401 3.6 29.0 1.0 CB A:MET252 3.7 45.1 1.0 CB A:HIS248 4.1 24.4 1.0 N A:MET252 4.2 40.6 1.0 CG A:HIS248 4.4 26.5 1.0 O A:SER249 4.5 33.4 1.0 C A:MET252 4.6 30.6 1.0 CG1 A:ILE337 4.6 26.3 1.0 CB A:ILE337 4.6 26.4 1.0 ND1 A:HIS248 4.7 23.9 1.0 SD A:MET252 4.7 74.1 1.0 CG2 A:ILE337 4.7 22.8 1.0 O A:MET252 4.8 28.2 1.0 NE2 A:HIS293 4.8 48.7 1.0 C1 A:86D401 4.8 25.5 1.0 CG A:HIS293 4.9 47.4 1.0 C4 A:86D401 5.0 31.2 1.0 CD2 A:LEU296 5.0 38.5 1.0 O A:HOH504 5.0 47.8 1.0

Fluorine binding site 3 out of 5 in the Crystal Structure of PT2399 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 PT2399 Bound to HIF2A-B*:Arnt-B* Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:32.4 occ:1.00 F2 A:86D401 0.0 32.4 1.0 C11 A:86D401 1.3 33.6 1.0 F5 A:86D401 2.2 31.8 1.0 C12 A:86D401 2.3 32.3 1.0 C15 A:86D401 2.4 27.7 1.0 CG2 A:ILE337 3.0 22.8 1.0 C13 A:86D401 3.0 29.0 1.0 C14 A:86D401 3.1 27.1 1.0 CB A:ILE337 3.3 26.4 1.0 SG A:CYS339 3.5 29.4 1.0 O4 A:86D401 3.5 33.5 1.0 CD1 A:ILE337 3.5 26.7 1.0 CB A:HIS248 3.7 24.4 1.0 CG A:HIS248 3.7 26.5 1.0 CG1 A:ILE337 3.9 26.3 1.0 CD2 A:HIS248 4.0 26.9 1.0 C1 A:86D401 4.2 25.5 1.0 C4 A:86D401 4.2 31.2 1.0 CD2 A:LEU296 4.4 38.5 1.0 O2 A:86D401 4.4 30.3 1.0 ND1 A:HIS248 4.5 23.9 1.0 CA A:ILE337 4.7 23.2 1.0 O1 A:86D401 4.8 25.5 1.0 NE2 A:HIS248 4.8 25.0 1.0 C A:ILE337 4.9 24.9 1.0 O A:ILE337 4.9 22.1 1.0 CE1 A:HIS293 5.0 51.0 1.0 ND1 A:HIS293 5.0 44.9 1.0 CE1 A:HIS248 5.0 21.6 1.0

Fluorine binding site 4 out of 5 in the Crystal Structure of PT2399 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 4 of Crystal Structure of PT2399 Bound to HIF2A-B*:Arnt-B* Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:50.5 occ:1.00 F3 A:86D401 0.0 50.5 1.0 C16 A:86D401 1.3 35.2 1.0 F4 A:86D401 2.1 53.6 1.0 S1 A:86D401 2.3 36.8 1.0 O3 A:86D401 2.6 32.9 1.0 CE A:MET289 3.1 29.5 1.0 C4 A:86D401 3.1 31.2 1.0 CB A:SER292 3.2 42.1 1.0 CB A:SER304 3.3 32.6 1.0 C3 A:86D401 3.4 27.9 1.0 O2 A:86D401 3.6 30.3 1.0 CA A:SER304 3.7 36.2 1.0 OG A:SER292 3.8 51.2 1.0 SD A:MET289 4.1 37.7 1.0 C13 A:86D401 4.2 29.0 1.0 CA A:SER292 4.4 48.2 1.0 C A:SER292 4.5 47.6 1.0 N A:HIS293 4.5 46.4 1.0 O A:MET289 4.5 44.7 1.0 N A:SER304 4.5 39.1 1.0 O A:HOH504 4.6 47.8 1.0 O4 A:86D401 4.6 33.5 1.0 C2 A:86D401 4.7 23.7 1.0 OG A:SER304 4.7 27.2 1.0 CA A:MET289 4.7 37.8 1.0 CG1 A:VAL302 4.9 50.9 1.0 C12 A:86D401 4.9 32.3 1.0 C A:SER304 4.9 42.0 1.0 CB A:MET289 4.9 35.6 1.0

Fluorine binding site 5 out of 5 in the Crystal Structure of PT2399 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 5 of Crystal Structure of PT2399 Bound to HIF2A-B*:Arnt-B* Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:53.6 occ:1.00 F4 A:86D401 0.0 53.6 1.0 C16 A:86D401 1.3 35.2 1.0 F3 A:86D401 2.1 50.5 1.0 S1 A:86D401 2.4 36.8 1.0 O4 A:86D401 2.6 33.5 1.0 C4 A:86D401 2.7 31.2 1.0 C13 A:86D401 3.0 29.0 1.0 O A:HOH504 3.0 47.8 1.0 O2 A:86D401 3.2 30.3 1.0 C12 A:86D401 3.3 32.3 1.0 C3 A:86D401 3.6 27.9 1.0 O3 A:86D401 3.6 32.9 1.0 N A:HIS293 3.8 46.4 1.0 O A:MET289 3.8 44.7 1.0 CE A:MET289 3.9 29.5 1.0 CA A:HIS293 4.0 45.5 1.0 C14 A:86D401 4.0 27.1 1.0 CB A:HIS293 4.1 40.7 1.0 CB A:SER292 4.1 42.1 1.0 OH A:TYR281 4.3 30.8 1.0 C A:SER292 4.3 47.6 1.0 ND1 A:HIS293 4.4 44.9 1.0 C2 A:86D401 4.5 23.7 1.0 C11 A:86D401 4.6 33.6 1.0 C1 A:86D401 4.6 25.5 1.0 C A:MET289 4.7 46.2 1.0 CG A:HIS293 4.7 47.4 1.0 CB A:MET289 4.8 35.6 1.0 CA A:MET289 4.8 37.8 1.0 CA A:SER292 4.9 48.2 1.0 O A:SER292 4.9 49.4 1.0 C15 A:86D401 4.9 27.7 1.0

H.Cho, X.Du, J.P.Rizzi, E.Liberzon, A.A.Chakraborty, W.Gao, I.Carvo, S.Signoretti, R.K.Bruick, J.A.Josey, E.M.Wallace, W.G.Kaelin. On-Target Efficacy of A Hif-2 Alpha Antagonist in Preclinical Kidney Cancer Models. Nature V. 539 107 2016.
ISSN: ISSN 0028-0836
PubMed: 27595393
DOI: 10.1038/NATURE19795