Fluorine in PDB 7jy3: Structure of Hba with Compound 23 (Pf-07059013)

The structure of Structure of Hba with Compound 23 (Pf-07059013), PDB code: 7jy3 was solved by J.Jasti, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.69 / 1.48
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.77, 82.47, 65.08, 90, 99.54, 90
R / Rfree (%)	18 / 20.7

The structure of Structure of Hba with Compound 23 (Pf-07059013) also contains other interesting chemical elements:

Iron

(Fe)

4 atoms

The binding sites of Fluorine atom in the Structure of Hba with Compound 23 (Pf-07059013) (pdb code 7jy3). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Structure of Hba with Compound 23 (Pf-07059013), PDB code: 7jy3:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Structure of Hba with Compound 23 (Pf-07059013)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of Hba with Compound 23 (Pf-07059013) within 5.0Å range: probe atom residue distance (Å) B Occ A:F204 b:24.1 occ:1.00 F27 A:VUD204 0.0 24.1 1.0 C20 A:VUD204 1.4 21.6 1.0 C19 A:VUD204 2.3 18.0 1.0 C21 A:VUD204 2.3 22.3 1.0 O A:HOH305 3.3 36.0 1.0 CG2 C:THR134 3.3 20.2 1.0 F27 C:VUD201 3.6 25.9 1.0 C22 A:VUD204 3.6 19.7 1.0 C18 A:VUD204 3.6 18.6 1.0 O C:HOH329 3.8 29.2 1.0 CG2 A:VAL1 3.8 29.5 1.0 C20 C:VUD201 3.9 21.6 1.0 CB C:THR134 3.9 19.4 1.0 O C:HOH322 4.0 30.0 1.0 C23 A:VUD204 4.1 17.0 1.0 C19 C:VUD201 4.2 18.9 1.0 N A:VAL1 4.4 28.2 1.0 C21 C:VUD201 4.5 20.1 1.0 OG1 C:THR134 4.7 18.8 1.0 CG2 C:VAL135 4.7 17.2 1.0 O A:HOH361 4.8 39.6 1.0 O C:SER131 4.8 17.2 1.0 CA A:VAL1 4.8 26.9 1.0 C17 A:VUD204 4.8 18.6 1.0 CB A:VAL1 4.9 30.0 1.0

Fluorine binding site 2 out of 2 in the Structure of Hba with Compound 23 (Pf-07059013)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of Hba with Compound 23 (Pf-07059013) within 5.0Å range: probe atom residue distance (Å) B Occ C:F201 b:25.9 occ:1.00 F27 C:VUD201 0.0 25.9 1.0 C20 C:VUD201 1.4 21.6 1.0 C19 C:VUD201 2.3 18.9 1.0 C21 C:VUD201 2.3 20.1 1.0 O C:HOH329 3.2 29.2 1.0 CG2 A:THR134 3.3 20.9 1.0 F27 A:VUD204 3.6 24.1 1.0 C22 C:VUD201 3.6 20.4 1.0 C18 C:VUD201 3.6 20.6 1.0 O A:HOH305 3.7 36.0 1.0 CG2 C:VAL1 3.8 22.9 1.0 C20 A:VUD204 3.9 21.6 1.0 CB A:THR134 3.9 19.5 1.0 C23 C:VUD201 4.1 22.4 1.0 C19 A:VUD204 4.1 18.0 1.0 O C:HOH322 4.2 30.0 1.0 N C:VAL1 4.3 21.9 1.0 C21 A:VUD204 4.5 22.3 1.0 OG1 A:THR134 4.7 19.9 1.0 CG2 A:VAL135 4.7 18.0 1.0 CA C:VAL1 4.7 20.2 1.0 O A:SER131 4.8 17.9 1.0 C17 C:VUD201 4.8 21.0 1.0 CB C:VAL1 4.8 22.7 1.0 O A:HOH361 5.0 39.6 1.0 C18 A:VUD204 5.0 18.6 1.0

A.Gopalsamy, A.E.Aulabaugh, A.Barakat, K.C.Beaumont, S.Cabral, D.P.Canterbury, A.Casimiro-Garcia, J.S.Chang, M.Z.Chen, C.Choi, R.L.Dow, O.O.Fadeyi, X.Feng, S.P.France, R.M.Howard, J.M.Janz, J.Jasti, R.Jasuja, L.H.Jones, A.King-Ahmad, K.M.Knee, J.T.Kohrt, C.Limberakis, S.Liras, C.A.Martinez, K.F.Mcclure, A.Narayanan, J.Narula, J.J.Novak, T.N.O'connell, M.D.Parikh, D.W.Piotrowski, O.Plotnikova, R.P.Robinson, P.V.Sahasrabudhe, R.Sharma, B.A.Thuma, D.Vasa, L.Wei, A.Z.Wenzel, J.M.Withka, J.Xiao, H.G.Yayla. Pf-07059013: A Noncovalent Modulator of Hemoglobin For Treatment of Sickle Cell Disease. J.Med.Chem. 2020.
ISSN: ISSN 0022-2623
PubMed: 33356244
DOI: 10.1021/ACS.JMEDCHEM.0C01518