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Fluorine in PDB 5f4u: Hiv-1 GP120 Complex with Bnm-IV-197

Protein crystallography data

The structure of Hiv-1 GP120 Complex with Bnm-IV-197, PDB code: 5f4u was solved by S.Liang, W.A.Hendrickson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.40 / 3.10
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 67.439, 128.123, 193.599, 90.00, 90.00, 90.00
R / Rfree (%) 21.8 / 28

Other elements in 5f4u:

The structure of Hiv-1 GP120 Complex with Bnm-IV-197 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Hiv-1 GP120 Complex with Bnm-IV-197 (pdb code 5f4u). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Hiv-1 GP120 Complex with Bnm-IV-197, PDB code: 5f4u:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 5f4u

Go back to Fluorine Binding Sites List in 5f4u
Fluorine binding site 1 out of 2 in the Hiv-1 GP120 Complex with Bnm-IV-197


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Hiv-1 GP120 Complex with Bnm-IV-197 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F507

b:20.0
occ:1.00
FAC A:5VH507 0.0 20.0 1.0
CAB A:5VH507 1.4 20.0 1.0
CAD A:5VH507 2.4 20.0 1.0
CAA A:5VH507 2.4 20.0 1.0
O A:SER375 2.9 74.6 1.0
CLAE A:5VH507 2.9 20.0 1.0
OG A:SER375 3.1 68.6 1.0
CG2 A:THR257 3.4 62.3 1.0
CE A:MET475 3.5 89.4 1.0
N A:THR257 3.6 76.4 1.0
CA A:SER256 3.6 87.9 1.0
C A:SER375 3.6 83.1 1.0
C A:SER256 3.6 85.2 1.0
CAH A:5VH507 3.6 20.0 1.0
CAF A:5VH507 3.6 20.0 1.0
CB A:SER375 3.8 56.5 1.0
OG1 A:THR257 4.0 68.0 1.0
N A:SER256 4.0 85.5 1.0
CAG A:5VH507 4.1 20.0 1.0
CB A:THR257 4.1 83.7 1.0
O A:SER256 4.2 79.0 1.0
CA A:SER375 4.3 87.1 1.0
N A:PHE376 4.3 73.9 1.0
O A:VAL255 4.3 95.6 1.0
CG1 A:VAL255 4.4 89.8 1.0
C A:VAL255 4.4 78.9 1.0
CA A:THR257 4.4 75.1 1.0
CA A:PHE376 4.5 82.8 1.0
OAK A:5VH507 4.6 20.0 1.0
NAI A:5VH507 4.7 20.0 1.0
O A:GLU370 4.8 83.3 1.0
SD A:MET475 4.8 77.3 1.0
N A:SER375 4.9 76.3 1.0
CB A:SER256 4.9 84.8 1.0

Fluorine binding site 2 out of 2 in 5f4u

Go back to Fluorine Binding Sites List in 5f4u
Fluorine binding site 2 out of 2 in the Hiv-1 GP120 Complex with Bnm-IV-197


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Hiv-1 GP120 Complex with Bnm-IV-197 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F508

b:20.0
occ:1.00
FAC B:5VH508 0.0 20.0 1.0
CAB B:5VH508 1.4 20.0 1.0
CAA B:5VH508 2.4 20.0 1.0
CAD B:5VH508 2.4 20.0 1.0
OG B:SER375 2.6 73.1 1.0
CLAE B:5VH508 2.9 20.0 1.0
O B:SER375 3.0 46.1 1.0
CG2 B:THR257 3.4 60.0 1.0
C B:SER375 3.5 59.7 1.0
CA B:SER256 3.6 66.4 1.0
CE B:MET475 3.6 74.8 1.0
C B:SER256 3.6 63.3 1.0
CB B:SER375 3.6 60.0 1.0
CAH B:5VH508 3.6 20.0 1.0
CAF B:5VH508 3.6 20.0 1.0
N B:THR257 3.7 69.1 1.0
OG1 B:THR257 3.9 56.5 1.0
N B:SER256 4.0 78.1 1.0
O B:SER256 4.1 88.0 1.0
CB B:THR257 4.1 55.3 1.0
CA B:SER375 4.1 64.0 1.0
N B:PHE376 4.1 60.8 1.0
CAG B:5VH508 4.1 20.0 1.0
CG1 B:VAL255 4.3 67.2 1.0
CA B:PHE376 4.4 70.0 1.0
C B:VAL255 4.4 77.1 1.0
O B:VAL255 4.4 83.2 1.0
CA B:THR257 4.5 57.4 1.0
OAK B:5VH508 4.5 20.0 1.0
O B:GLU370 4.6 47.9 1.0
NAI B:5VH508 4.7 20.0 1.0
N B:SER375 4.8 65.1 1.0
CB B:SER256 4.9 83.6 1.0
SD B:MET475 5.0 81.4 1.0

Reference:

B.Melillo, S.Liang, J.Park, A.Schon, J.R.Courter, J.M.Lalonde, D.J.Wendler, A.M.Princiotto, M.S.Seaman, E.Freire, J.Sodroski, N.Madani, W.A.Hendrickson, A.B.Smith. Small-Molecule CD4-Mimics: Structure-Based Optimization of Hiv-1 Entry Inhibition. Acs Med Chem Lett V. 7 330 2016.
ISSN: ISSN 1948-5875
PubMed: 26985324
DOI: 10.1021/ACSMEDCHEMLETT.5B00471
Page generated: Sun Dec 13 12:22:08 2020

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