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

Protein crystallography data

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

Other elements in 4ijh:

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

Fluorine Binding Sites:

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 4ijh

Go back to Fluorine Binding Sites List in 4ijh
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 4ijh

Go back to Fluorine Binding Sites List in 4ijh
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 4ijh

Go back to Fluorine Binding Sites List in 4ijh
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 4ijh

Go back to Fluorine Binding Sites List in 4ijh
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 4ijh

Go back to Fluorine Binding Sites List in 4ijh
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

Reference:

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
Page generated: Sun Dec 13 12:04:35 2020

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