Fluorine in PDB 3e2m: Lfa-1 I Domain Bound to Inhibitors

The structure of Lfa-1 I Domain Bound to Inhibitors, PDB code: 3e2m was solved by L.F.Silvian, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.43 / 2.00
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	73.062, 69.608, 72.363, 90.00, 90.00, 90.00
R / Rfree (%)	21.5 / 28.7

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Fluorine atom in the Lfa-1 I Domain Bound to Inhibitors (pdb code 3e2m). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 12 binding sites of Fluorine where determined in the Lfa-1 I Domain Bound to Inhibitors, PDB code: 3e2m:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 12 in the Lfa-1 I Domain Bound to Inhibitors


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Lfa-1 I Domain Bound to Inhibitors within 5.0Å range: probe atom residue distance (Å) B Occ A:F1 b:27.4 occ:1.00 F6 A:E2M1 0.0 27.4 1.0 C1 A:E2M1 1.3 21.6 1.0 F1 A:E2M1 2.2 28.2 1.0 F2 A:E2M1 2.2 29.8 1.0 C2 A:E2M1 2.3 30.2 1.0 F3 A:E2M1 2.3 26.8 1.0 F4 A:E2M1 2.3 27.8 1.0 C29 A:E2M1 2.5 24.2 1.0 C28 A:E2M1 2.8 26.1 1.0 C3 A:E2M1 3.5 20.6 1.0 CG1 A:ILE235 3.8 19.4 1.0 F5 A:E2M1 3.9 26.5 1.0 CE2 A:PHE134 3.9 20.3 1.0 CG1 A:VAL157 4.0 15.7 1.0 CG2 A:VAL157 4.0 16.3 1.0 C20 A:E2M1 4.1 21.2 1.0 S A:E2M1 4.1 28.6 1.0 CG2 A:ILE235 4.2 18.9 1.0 CD1 A:ILE235 4.3 17.7 1.0 CZ A:PHE134 4.3 19.7 1.0 CE2 A:PHE153 4.4 18.7 1.0 CB A:VAL157 4.5 17.5 1.0 CB A:ILE235 4.5 19.9 1.0 CZ A:PHE153 4.6 18.8 1.0 C18 A:E2M1 4.6 27.9 1.0 CD1 A:LEU302 4.6 24.1 1.0 C19 A:E2M1 4.9 27.8 1.0 CD2 A:PHE134 4.9 20.7 1.0

Fluorine binding site 2 out of 12 in the Lfa-1 I Domain Bound to Inhibitors


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Lfa-1 I Domain Bound to Inhibitors within 5.0Å range: probe atom residue distance (Å) B Occ A:F1 b:28.2 occ:1.00 F1 A:E2M1 0.0 28.2 1.0 C1 A:E2M1 1.3 21.6 1.0 F2 A:E2M1 2.2 29.8 1.0 F6 A:E2M1 2.2 27.4 1.0 C2 A:E2M1 2.3 30.2 1.0 S A:E2M1 2.4 28.6 1.0 C3 A:E2M1 2.7 20.6 1.0 CE2 A:PHE153 3.5 18.7 1.0 CZ A:PHE153 3.5 18.8 1.0 C28 A:E2M1 3.6 26.1 1.0 CD1 A:ILE259 3.7 20.6 1.0 CG2 A:ILE235 3.8 18.9 1.0 F3 A:E2M1 3.9 26.8 1.0 C4 A:E2M1 4.0 23.6 1.0 C18 A:E2M1 4.0 27.9 1.0 C29 A:E2M1 4.1 24.2 1.0 F4 A:E2M1 4.2 27.8 1.0 CG1 A:ILE235 4.4 19.4 1.0 CD1 A:ILE235 4.6 17.7 1.0 CD1 A:LEU302 4.6 24.1 1.0 CD2 A:LEU298 4.6 20.4 1.0 C20 A:E2M1 4.7 21.2 1.0 CB A:ILE235 4.7 19.9 1.0 C17 A:E2M1 4.7 28.0 1.0 CG1 A:ILE259 4.8 20.0 1.0 CD2 A:PHE153 4.8 18.5 1.0 CE1 A:PHE153 4.9 18.2 1.0 C19 A:E2M1 4.9 27.8 1.0 O1 A:E2M1 5.0 27.9 1.0

Fluorine binding site 3 out of 12 in the Lfa-1 I Domain Bound to Inhibitors


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Lfa-1 I Domain Bound to Inhibitors within 5.0Å range: probe atom residue distance (Å) B Occ A:F1 b:29.8 occ:1.00 F2 A:E2M1 0.0 29.8 1.0 C1 A:E2M1 1.3 21.6 1.0 F1 A:E2M1 2.2 28.2 1.0 F6 A:E2M1 2.2 27.4 1.0 C2 A:E2M1 2.3 30.2 1.0 F3 A:E2M1 2.4 26.8 1.0 CD1 A:LEU302 2.7 24.1 1.0 C28 A:E2M1 3.1 26.1 1.0 C29 A:E2M1 3.2 24.2 1.0 C3 A:E2M1 3.2 20.6 1.0 CG A:LEU302 3.4 24.6 1.0 S A:E2M1 3.6 28.6 1.0 CZ A:PHE153 3.6 18.8 1.0 CG2 A:VAL157 3.8 16.3 1.0 F4 A:E2M1 3.8 27.8 1.0 CE2 A:PHE153 4.1 18.7 1.0 F5 A:E2M1 4.3 26.5 1.0 C20 A:E2M1 4.3 21.2 1.0 CB A:LEU302 4.3 24.0 1.0 CG1 A:VAL157 4.4 15.7 1.0 C18 A:E2M1 4.4 27.9 1.0 CD2 A:LEU302 4.5 23.8 1.0 CE1 A:PHE153 4.6 18.2 1.0 CB A:VAL157 4.8 17.5 1.0 C19 A:E2M1 4.9 27.8 1.0

Fluorine binding site 4 out of 12 in the Lfa-1 I Domain Bound to Inhibitors


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Lfa-1 I Domain Bound to Inhibitors within 5.0Å range: probe atom residue distance (Å) B Occ A:F1 b:26.5 occ:1.00 F5 A:E2M1 0.0 26.5 1.0 C29 A:E2M1 1.3 24.2 1.0 F4 A:E2M1 2.2 27.8 1.0 F3 A:E2M1 2.2 26.8 1.0 C28 A:E2M1 2.3 26.1 1.0 C21 A:E2M1 2.3 33.1 1.0 C20 A:E2M1 2.7 21.2 1.0 C22 A:E2M1 3.5 25.9 1.0 C2 A:E2M1 3.6 30.2 1.0 CG2 B:VAL308 3.6 23.1 1.0 CB B:VAL308 3.7 22.9 1.0 F6 A:E2M1 3.9 27.4 1.0 O5 A:E2M1 3.9 28.1 1.0 CG1 B:VAL308 4.0 21.9 1.0 C19 A:E2M1 4.0 27.8 1.0 CD1 A:LEU132 4.1 18.5 1.0 CD1 A:LEU161 4.1 20.2 1.0 C23 A:E2M1 4.1 28.5 1.0 C1 A:E2M1 4.1 21.6 1.0 F2 A:E2M1 4.3 29.8 1.0 CE2 A:TYR166 4.4 21.2 1.0 CG1 A:VAL157 4.4 15.7 1.0 OH A:TYR166 4.7 21.7 1.0 C3 A:E2M1 4.7 20.6 1.0 CZ A:TYR166 4.8 21.6 1.0 C18 A:E2M1 4.9 27.9 1.0

Fluorine binding site 5 out of 12 in the Lfa-1 I Domain Bound to Inhibitors


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Lfa-1 I Domain Bound to Inhibitors within 5.0Å range: probe atom residue distance (Å) B Occ A:F1 b:27.8 occ:1.00 F4 A:E2M1 0.0 27.8 1.0 C29 A:E2M1 1.3 24.2 1.0 F5 A:E2M1 2.2 26.5 1.0 F3 A:E2M1 2.2 26.8 1.0 C28 A:E2M1 2.3 26.1 1.0 F6 A:E2M1 2.3 27.4 1.0 C2 A:E2M1 3.1 30.2 1.0 CD1 A:LEU132 3.1 18.5 1.0 C1 A:E2M1 3.2 21.6 1.0 C20 A:E2M1 3.2 21.2 1.0 C21 A:E2M1 3.5 33.1 1.0 CG1 A:ILE235 3.7 19.4 1.0 F2 A:E2M1 3.8 29.8 1.0 CG1 A:VAL157 4.0 15.7 1.0 CD1 A:ILE235 4.0 17.7 1.0 CD2 A:LEU132 4.0 18.2 1.0 CG A:LEU132 4.2 18.4 1.0 F1 A:E2M1 4.2 28.2 1.0 C3 A:E2M1 4.3 20.6 1.0 C19 A:E2M1 4.4 27.8 1.0 CZ A:PHE134 4.6 19.7 1.0 C22 A:E2M1 4.6 25.9 1.0 CE2 A:PHE134 4.7 20.3 1.0 C18 A:E2M1 4.9 27.9 1.0

Fluorine binding site 6 out of 12 in the Lfa-1 I Domain Bound to Inhibitors


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Lfa-1 I Domain Bound to Inhibitors within 5.0Å range: probe atom residue distance (Å) B Occ A:F1 b:26.8 occ:1.00 F3 A:E2M1 0.0 26.8 1.0 C29 A:E2M1 1.3 24.2 1.0 F5 A:E2M1 2.2 26.5 1.0 F4 A:E2M1 2.2 27.8 1.0 C28 A:E2M1 2.3 26.1 1.0 F6 A:E2M1 2.3 27.4 1.0 F2 A:E2M1 2.4 29.8 1.0 C1 A:E2M1 2.6 21.6 1.0 C2 A:E2M1 2.8 30.2 1.0 CG1 A:VAL157 3.1 15.7 1.0 C20 A:E2M1 3.5 21.2 1.0 CD1 A:LEU302 3.9 24.1 1.0 F1 A:E2M1 3.9 28.2 1.0 CG A:LEU302 4.0 24.6 1.0 C21 A:E2M1 4.0 33.1 1.0 CG2 A:VAL157 4.0 16.3 1.0 C3 A:E2M1 4.1 20.6 1.0 CB A:VAL157 4.2 17.5 1.0 CD2 A:LEU302 4.4 23.8 1.0 CG2 B:VAL308 4.5 23.1 1.0 CD1 A:LEU161 4.6 20.2 1.0 C19 A:E2M1 4.6 27.8 1.0 C18 A:E2M1 4.9 27.9 1.0 CG1 B:VAL308 4.9 21.9 1.0

Fluorine binding site 7 out of 12 in the Lfa-1 I Domain Bound to Inhibitors


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Lfa-1 I Domain Bound to Inhibitors within 5.0Å range: probe atom residue distance (Å) B Occ B:F1 b:25.3 occ:1.00 F6 B:E2M1 0.0 25.3 1.0 C1 B:E2M1 1.3 23.0 1.0 F1 B:E2M1 2.2 26.6 1.0 F2 B:E2M1 2.2 25.3 1.0 C2 B:E2M1 2.3 25.1 1.0 F3 B:E2M1 2.3 24.5 1.0 F4 B:E2M1 2.4 24.6 1.0 C29 B:E2M1 2.6 23.4 1.0 C28 B:E2M1 2.8 24.0 1.0 C3 B:E2M1 3.5 23.0 1.0 CE2 B:PHE134 3.8 18.6 1.0 CG2 B:VAL157 3.9 19.3 1.0 F5 B:E2M1 3.9 23.0 1.0 CG1 B:ILE235 3.9 20.5 1.0 CG1 B:VAL157 4.0 18.2 1.0 C20 B:E2M1 4.1 22.8 1.0 S B:E2M1 4.1 24.5 1.0 CZ B:PHE134 4.2 16.3 1.0 CD1 B:ILE235 4.2 20.7 1.0 CE2 B:PHE153 4.3 20.7 1.0 O B:HOH476 4.4 0.6 1.0 CB B:VAL157 4.4 19.3 1.0 CG2 B:ILE235 4.4 20.0 1.0 CZ B:PHE153 4.6 20.7 1.0 C18 B:E2M1 4.6 23.6 1.0 CB B:ILE235 4.7 20.2 1.0 CD2 B:PHE134 4.8 17.6 1.0 CD2 B:LEU302 4.9 26.0 1.0 C19 B:E2M1 4.9 24.8 1.0

Fluorine binding site 8 out of 12 in the Lfa-1 I Domain Bound to Inhibitors


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Lfa-1 I Domain Bound to Inhibitors within 5.0Å range: probe atom residue distance (Å) B Occ B:F1 b:26.6 occ:1.00 F1 B:E2M1 0.0 26.6 1.0 C1 B:E2M1 1.3 23.0 1.0 F6 B:E2M1 2.2 25.3 1.0 F2 B:E2M1 2.2 25.3 1.0 C2 B:E2M1 2.3 25.1 1.0 S B:E2M1 2.4 24.5 1.0 C3 B:E2M1 2.7 23.0 1.0 CE2 B:PHE153 3.3 20.7 1.0 CZ B:PHE153 3.4 20.7 1.0 C28 B:E2M1 3.6 24.0 1.0 CG2 B:ILE235 3.8 20.0 1.0 F3 B:E2M1 3.9 24.5 1.0 CD1 B:ILE259 4.0 19.6 1.0 C4 B:E2M1 4.0 22.9 1.0 C18 B:E2M1 4.0 23.6 1.0 C29 B:E2M1 4.1 23.4 1.0 F4 B:E2M1 4.3 24.6 1.0 CG1 B:ILE235 4.4 20.5 1.0 CD1 B:ILE235 4.4 20.7 1.0 CD2 B:PHE153 4.7 20.6 1.0 O B:HOH476 4.7 0.6 1.0 CD2 B:LEU302 4.7 26.0 1.0 C20 B:E2M1 4.7 22.8 1.0 CB B:ILE235 4.7 20.2 1.0 CE1 B:PHE153 4.8 20.6 1.0 C17 B:E2M1 4.8 24.8 1.0 CG2 B:VAL157 4.9 19.3 1.0 C19 B:E2M1 4.9 24.8 1.0 CD2 B:LEU298 4.9 20.7 1.0 O1 B:E2M1 4.9 23.6 1.0 C5 B:E2M1 5.0 23.9 1.0 CE2 B:PHE134 5.0 18.6 1.0

Fluorine binding site 9 out of 12 in the Lfa-1 I Domain Bound to Inhibitors


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Lfa-1 I Domain Bound to Inhibitors within 5.0Å range: probe atom residue distance (Å) B Occ B:F1 b:25.3 occ:1.00 F2 B:E2M1 0.0 25.3 1.0 C1 B:E2M1 1.3 23.0 1.0 F1 B:E2M1 2.2 26.6 1.0 F6 B:E2M1 2.2 25.3 1.0 C2 B:E2M1 2.3 25.1 1.0 F3 B:E2M1 2.4 24.5 1.0 CD2 B:LEU302 2.9 26.0 1.0 O B:HOH476 3.1 0.6 1.0 C28 B:E2M1 3.1 24.0 1.0 C29 B:E2M1 3.2 23.4 1.0 C3 B:E2M1 3.2 23.0 1.0 S B:E2M1 3.6 24.5 1.0 CZ B:PHE153 3.6 20.7 1.0 CG2 B:VAL157 3.7 19.3 1.0 F4 B:E2M1 3.8 24.6 1.0 CG B:LEU302 3.9 23.7 1.0 CE2 B:PHE153 4.1 20.7 1.0 CD1 B:LEU302 4.2 23.7 1.0 CB B:LEU302 4.3 23.8 1.0 F5 B:E2M1 4.3 23.0 1.0 C20 B:E2M1 4.3 22.8 1.0 C18 B:E2M1 4.4 23.6 1.0 CG1 B:VAL157 4.5 18.2 1.0 CE1 B:PHE153 4.6 20.6 1.0 CB B:VAL157 4.7 19.3 1.0 C19 B:E2M1 4.9 24.8 1.0

Fluorine binding site 10 out of 12 in the Lfa-1 I Domain Bound to Inhibitors


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Lfa-1 I Domain Bound to Inhibitors within 5.0Å range: probe atom residue distance (Å) B Occ B:F1 b:23.0 occ:1.00 F5 B:E2M1 0.0 23.0 1.0 C29 B:E2M1 1.3 23.4 1.0 F3 B:E2M1 2.2 24.5 1.0 F4 B:E2M1 2.2 24.6 1.0 C28 B:E2M1 2.3 24.0 1.0 C21 B:E2M1 2.3 26.4 1.0 C20 B:E2M1 2.7 22.8 1.0 O B:HOH476 3.5 0.6 1.0 C2 B:E2M1 3.6 25.1 1.0 C22 B:E2M1 3.6 26.6 1.0 CG2 A:VAL308 3.7 18.7 1.0 O5 B:E2M1 3.9 26.7 1.0 F6 B:E2M1 3.9 25.3 1.0 CB A:VAL308 3.9 19.9 1.0 C19 B:E2M1 4.0 24.8 1.0 CD1 B:LEU161 4.1 19.9 1.0 CD1 B:LEU132 4.1 15.8 1.0 C1 B:E2M1 4.1 23.0 1.0 C23 B:E2M1 4.2 27.4 1.0 F2 B:E2M1 4.3 25.3 1.0 CE2 B:TYR166 4.3 17.5 1.0 CG1 A:VAL308 4.3 19.4 1.0 OH B:TYR166 4.5 19.6 1.0 CG1 B:VAL157 4.6 18.2 1.0 C3 B:E2M1 4.7 23.0 1.0 CZ B:TYR166 4.7 18.9 1.0 C18 B:E2M1 4.9 23.6 1.0

E.Y.Lin, K.M.Guckian, L.Silvian, D.Chin, P.A.Boriack-Sjodin, H.Van Vlijmen, J.E.Friedman, D.M.Scott. Structure-Activity Relationship of Ortho- and Meta-Phenol Based Lfa-1 Icam Inhibitors Bioorg.Med.Chem.Lett. V. 18 5245 2008.
ISSN: ISSN 0960-894X
PubMed: 18783948
DOI: 10.1016/J.BMCL.2008.08.062