Fluorine in PDB 4ijh: Fragment-Based Discovery of Protein-Protein Interaction Inhibitors of Replication Protein A

The structure of Fragment-Based Discovery of Protein-Protein Interaction Inhibitors of Replication Protein A, PDB code: 4ijh was solved by M.D.Feldkamp, J.D.Patrone, J.P.Kennedy, A.O.Frank, B.Vangamudi, N.F.Pelz, O.W.Rossanese, A.G.Waterson, S.W.Fesik, W.J.Chazin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.87 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	37.871, 52.629, 54.518, 90.00, 90.00, 90.00
R / Rfree (%)	14.9 / 18.9

The structure of Fragment-Based Discovery of Protein-Protein Interaction Inhibitors of Replication Protein A also contains other interesting chemical elements:

Chlorine

(Cl)

5 atoms

The binding sites of Fluorine atom in the Fragment-Based Discovery of Protein-Protein Interaction Inhibitors of Replication Protein A (pdb code 4ijh). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 5 binding sites of Fluorine where determined in the Fragment-Based Discovery of Protein-Protein Interaction Inhibitors of Replication Protein A, PDB code: 4ijh:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5;

Fluorine binding site 1 out of 5 in the Fragment-Based Discovery of Protein-Protein Interaction Inhibitors of Replication Protein A


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Fragment-Based Discovery of Protein-Protein Interaction Inhibitors of Replication Protein A within 5.0Å range: probe atom residue distance (Å) B Occ A:F201 b:9.3 occ:1.00 F26 A:1EJ201 0.0 9.3 1.0 C02 A:1EJ201 1.3 7.3 1.0 C01 A:1EJ201 2.3 5.2 1.0 C03 A:1EJ201 2.4 6.8 1.0 H011 A:1EJ201 2.5 6.3 1.0 H031 A:1EJ201 2.6 8.2 1.0 HA A:SER55 2.6 11.2 0.5 HA A:SER55 2.7 11.0 0.5 HG3 A:ARG43 2.7 6.5 1.0 HG3 A:MET57 2.9 8.7 0.8 HD2 A:ARG43 2.9 7.0 0.9 HG2 A:MET57 2.9 8.0 0.2 HG13 A:VAL93 3.1 11.2 0.9 NE A:ARG43 3.1 7.6 1.0 HE A:ARG43 3.3 9.2 0.9 CD A:ARG43 3.3 5.8 0.9 CG A:ARG43 3.4 5.4 1.0 HG22 A:VAL93 3.5 10.1 0.8 CA A:SER55 3.5 9.3 0.5 CA A:SER55 3.5 9.2 0.5 C06 A:1EJ201 3.6 4.7 1.0 CG A:MET57 3.6 6.7 0.2 C04 A:1EJ201 3.6 6.6 1.0 SD A:MET57 3.6 5.6 0.2 C A:SER55 3.7 8.8 1.0 CG A:MET57 3.7 7.2 0.8 CZ A:ARG43 3.7 9.2 0.9 O A:SER54 3.8 9.8 1.0 O A:PHE56 3.8 3.9 1.0 HB2 A:SER55 3.8 13.9 0.5 HG2 A:MET57 3.8 8.7 0.8 HG3 A:MET57 3.9 8.0 0.2 CG1 A:VAL93 4.0 9.3 0.9 HG11 A:VAL93 4.0 11.2 0.9 O A:SER55 4.0 11.6 1.0 N A:PHE56 4.0 5.0 1.0 HB2 A:ARG43 4.1 5.7 1.0 HG2 A:ARG43 4.1 6.5 1.0 C05 A:1EJ201 4.1 6.2 1.0 HB3 A:SER55 4.1 13.8 0.5 CB A:SER55 4.2 11.6 0.5 C A:PHE56 4.2 4.4 1.0 NH1 A:ARG43 4.2 9.8 1.0 HH11 A:ARG43 4.2 11.8 0.9 HD3 A:ARG43 4.2 7.0 0.9 SD A:MET57 4.2 7.2 0.8 NH2 A:ARG43 4.2 9.3 0.9 CG2 A:VAL93 4.2 8.4 0.8 H A:PHE56 4.3 6.0 1.0 HH21 A:ARG43 4.3 11.1 0.9 HG21 A:VAL93 4.3 10.1 0.8 CB A:SER55 4.3 11.5 0.5 CB A:ARG43 4.3 4.8 1.0 H061 A:1EJ201 4.4 5.6 1.0 H041 A:1EJ201 4.4 8.0 1.0 HB3 A:SER55 4.5 13.9 0.5 N A:SER55 4.6 6.0 1.0 HA A:VAL93 4.6 5.9 1.0 C A:SER54 4.6 8.8 1.0 OG A:SER55 4.6 11.4 0.5 HA A:ARG43 4.6 4.7 1.0 HG12 A:VAL93 4.7 11.2 0.9 CB A:VAL93 4.7 7.1 1.0 CA A:PHE56 4.7 4.0 1.0 HH12 A:ARG43 4.8 11.8 0.9 N A:MET57 4.8 4.4 1.0 HH22 A:ARG43 4.8 11.1 0.9 CB A:MET57 4.9 6.4 0.8 CB A:MET57 4.9 6.2 0.2

Fluorine binding site 2 out of 5 in the Fragment-Based Discovery of Protein-Protein Interaction Inhibitors of Replication Protein A


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Fragment-Based Discovery of Protein-Protein Interaction Inhibitors of Replication Protein A within 5.0Å range: probe atom residue distance (Å) B Occ A:F202 b:22.6 occ:0.80 F26 A:1EJ202 0.0 22.6 0.8 C02 A:1EJ202 1.3 18.5 0.7 C03 A:1EJ202 2.3 16.4 0.8 C01 A:1EJ202 2.4 14.7 0.9 H031 A:1EJ202 2.5 19.6 0.8 H011 A:1EJ202 2.6 17.7 0.9 H171 A:1EJ203 3.0 17.7 0.9 C04 A:1EJ202 3.6 13.3 0.8 C06 A:1EJ202 3.6 13.2 0.9 H161 A:1EJ203 3.6 15.9 1.0 C17 A:1EJ203 3.8 14.7 0.9 H011 A:1EJ203 4.0 24.9 0.8 H061 A:1EJ203 4.0 26.3 0.7 C06 A:1EJ203 4.0 21.9 0.7 C01 A:1EJ203 4.0 20.8 0.8 C05 A:1EJ202 4.1 11.4 1.0 C16 A:1EJ203 4.1 13.2 1.0 H041 A:1EJ202 4.4 15.9 0.8 H061 A:1EJ202 4.4 15.8 0.9 C02 A:1EJ203 4.6 19.5 0.5 C05 A:1EJ203 4.6 23.3 0.9 O A:HOH425 4.7 32.9 1.0 CL2 A:1EJ204 4.9 16.1 0.9

Fluorine binding site 3 out of 5 in the Fragment-Based Discovery of Protein-Protein Interaction Inhibitors of Replication Protein A


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Fragment-Based Discovery of Protein-Protein Interaction Inhibitors of Replication Protein A within 5.0Å range: probe atom residue distance (Å) B Occ A:F203 b:15.2 occ:1.00 F26 A:1EJ203 0.0 15.2 1.0 C02 A:1EJ203 1.4 19.5 0.5 C01 A:1EJ203 2.4 20.8 0.8 C03 A:1EJ203 2.4 20.5 0.8 H011 A:1EJ203 2.6 24.9 0.8 H031 A:1EJ203 2.6 24.6 0.8 H161 A:1EJ204 2.8 14.2 0.8 H011 A:1EJ202 2.9 17.7 0.9 H161 A:1EJ201 3.0 6.6 1.0 H171 A:1EJ204 3.3 12.6 0.9 O A:HOH424 3.4 35.5 1.0 C16 A:1EJ204 3.5 11.8 0.8 C06 A:1EJ203 3.6 21.9 0.7 CL2 A:1EJ201 3.7 6.8 1.0 C04 A:1EJ203 3.7 21.7 1.0 C16 A:1EJ201 3.8 5.5 1.0 C17 A:1EJ204 3.8 10.5 0.9 C01 A:1EJ202 3.8 14.7 0.9 H061 A:1EJ202 3.8 15.8 0.9 O A:HOH427 3.9 34.5 1.0 C05 A:1EJ203 4.2 23.3 0.9 C06 A:1EJ202 4.2 13.2 0.9 H061 A:1EJ203 4.4 26.3 0.7 H041 A:1EJ203 4.5 26.0 1.0 H161 A:1EJ202 4.5 7.4 1.0 C15 A:1EJ201 4.5 5.8 1.0 H171 A:1EJ201 4.5 7.5 0.9 C21 A:1EJ201 4.6 6.1 1.0 C17 A:1EJ201 4.6 6.2 0.9 C16 A:1EJ202 4.6 6.2 1.0 O A:THR34 4.6 9.6 1.0 C15 A:1EJ204 4.8 12.1 0.9 CL2 A:1EJ204 4.8 16.1 0.9 C15 A:1EJ202 4.9 6.6 1.0 C02 A:1EJ202 4.9 18.5 0.7

Fluorine binding site 4 out of 5 in the Fragment-Based Discovery of Protein-Protein Interaction Inhibitors of Replication Protein A


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Fragment-Based Discovery of Protein-Protein Interaction Inhibitors of Replication Protein A within 5.0Å range: probe atom residue distance (Å) B Occ A:F204 b:11.7 occ:0.85 F26 A:1EJ204 0.0 11.7 0.8 C02 A:1EJ204 1.3 12.2 1.0 C01 A:1EJ204 2.4 12.7 0.9 C03 A:1EJ204 2.4 11.1 0.9 H011 A:1EJ204 2.6 15.2 0.9 H031 A:1EJ204 2.6 13.3 0.9 HG11 A:VAL93 2.8 11.2 0.9 HD11 A:ILE95 2.8 15.1 1.0 HB A:VAL93 2.8 8.6 1.0 HD11 A:LEU87 3.0 10.5 1.0 HG21 A:VAL93 3.0 10.1 0.8 CB A:VAL93 3.4 7.1 1.0 CG1 A:VAL93 3.4 9.3 0.9 C06 A:1EJ204 3.6 10.8 0.9 CG2 A:VAL93 3.6 8.4 0.8 C04 A:1EJ204 3.6 8.4 1.0 HG12 A:VAL93 3.7 11.2 0.9 CD1 A:ILE95 3.7 12.6 1.0 HG3 A:MET57 3.7 8.0 0.2 CD1 A:LEU87 3.8 8.8 1.0 HB2 A:ASN85 3.8 6.9 1.0 HG12 A:ILE95 3.8 10.5 1.0 HD13 A:LEU87 3.9 10.5 1.0 HG23 A:VAL93 4.0 10.1 0.8 SD A:MET57 4.1 7.2 0.8 HD13 A:ILE95 4.1 15.1 1.0 C05 A:1EJ204 4.1 9.5 1.0 HD12 A:LEU87 4.1 10.5 1.0 HG13 A:ILE95 4.1 10.5 1.0 CG1 A:ILE95 4.2 8.8 1.0 HG13 A:VAL93 4.3 11.2 0.9 HB3 A:ASN85 4.3 6.9 1.0 HD21 A:ASN85 4.3 9.1 1.0 HD12 A:ILE95 4.4 15.1 1.0 H061 A:1EJ204 4.4 12.9 0.9 HG22 A:VAL93 4.4 10.1 0.8 H041 A:1EJ204 4.4 10.1 1.0 HD21 A:LEU87 4.4 6.7 0.8 CB A:ASN85 4.5 5.7 1.0 CG A:MET57 4.7 6.7 0.2 HB2 A:MET57 4.7 7.7 0.8 HB2 A:MET57 4.7 7.5 0.2 CA A:VAL93 4.8 4.9 1.0 CG A:LEU87 5.0 5.8 1.0

Fluorine binding site 5 out of 5 in the Fragment-Based Discovery of Protein-Protein Interaction Inhibitors of Replication Protein A


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Fragment-Based Discovery of Protein-Protein Interaction Inhibitors of Replication Protein A within 5.0Å range: probe atom residue distance (Å) B Occ A:F205 b:12.4 occ:0.97 F26 A:1EJ205 0.0 12.4 1.0 C02 A:1EJ205 1.3 12.4 0.9 C03 A:1EJ205 2.3 11.3 1.0 C01 A:1EJ205 2.4 10.1 1.0 H031 A:1EJ205 2.5 13.6 1.0 H011 A:1EJ205 2.6 12.1 1.0 C04 A:1EJ205 3.6 10.2 0.9 C06 A:1EJ205 3.6 9.1 1.0 C05 A:1EJ205 4.1 7.4 1.0 O A:HOH417 4.1 18.1 1.0 H041 A:1EJ205 4.4 12.2 0.9 H061 A:1EJ205 4.4 10.9 1.0

J.D.Patrone, J.P.Kennedy, A.O.Frank, M.D.Feldkamp, B.Vangamudi, N.F.Pelz, O.W.Rossanese, A.G.Waterson, W.J.Chazin, S.W.Fesik. Discovery of Protein-Protein Interaction Inhibitors of Replication Protein A. Acs Med.Chem.Lett. V. 4 601 2013.
ISSN: ISSN 1948-5875
PubMed: 23914285
DOI: 10.1021/ML400032Y