Fluorine in PDB 6dd0: Crystal Structure of Vim-2 Complexed with Compound 8

Protein crystallography data

The structure of Crystal Structure of Vim-2 Complexed with Compound 8, PDB code: 6dd0 was solved by O.A.Pemberton, Y.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.39 / 1.50
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 102.630, 79.130, 67.790, 90.00, 130.50, 90.00
R / Rfree (%) 18.3 / 22.5

Other elements in 6dd0:

The structure of Crystal Structure of Vim-2 Complexed with Compound 8 also contains other interesting chemical elements:

Zinc (Zn) 6 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Vim-2 Complexed with Compound 8 (pdb code 6dd0). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of Vim-2 Complexed with Compound 8, PDB code: 6dd0:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 6dd0

Go back to Fluorine Binding Sites List in 6dd0
Fluorine binding site 1 out of 4 in the Crystal Structure of Vim-2 Complexed with Compound 8


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Vim-2 Complexed with Compound 8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F403

b:34.6
occ:0.83
F12 A:P9T403 0.0 34.6 0.8
C11 A:P9T403 1.4 33.8 0.8
C13 A:P9T403 2.4 33.9 0.8
C10 A:P9T403 2.4 29.3 0.8
C05 A:P9T403 2.7 20.1 0.8
C04 A:P9T403 2.8 23.8 0.8
O A:HOH705 3.4 34.5 1.0
CE2 A:PHE61 3.4 45.0 1.0
C14 A:P9T403 3.7 35.2 0.8
C17 A:P9T403 3.7 31.8 0.8
CD2 A:PHE61 3.7 44.8 1.0
P06 A:P9T403 3.9 19.3 0.8
O09 A:P9T403 3.9 18.3 0.8
O A:HOH664 4.0 21.4 1.0
CZ2 A:TRP87 4.1 13.7 1.0
C16 A:P9T403 4.1 33.9 0.8
C03 A:P9T403 4.2 27.7 0.8
ND2 A:ASN233 4.4 43.4 1.0
O07 A:P9T403 4.4 13.3 0.8
CH2 A:TRP87 4.4 14.5 1.0
CZ A:PHE61 4.5 44.9 1.0
F15 A:P9T403 4.8 38.4 0.8
O18 A:P9T403 4.8 31.8 0.8
CG A:PHE61 4.9 45.6 1.0
CG A:ASN233 4.9 42.0 1.0

Fluorine binding site 2 out of 4 in 6dd0

Go back to Fluorine Binding Sites List in 6dd0
Fluorine binding site 2 out of 4 in the Crystal Structure of Vim-2 Complexed with Compound 8


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Vim-2 Complexed with Compound 8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F403

b:38.4
occ:0.83
F15 A:P9T403 0.0 38.4 0.8
C14 A:P9T403 1.4 35.2 0.8
C16 A:P9T403 2.4 33.9 0.8
C13 A:P9T403 2.4 33.9 0.8
C11 A:P9T403 3.7 33.8 0.8
C17 A:P9T403 3.7 31.8 0.8
CB A:ASN233 3.9 39.7 1.0
C10 A:P9T403 4.2 29.3 0.8
OH A:TYR67 4.4 29.4 1.0
CG A:ASN233 4.7 42.0 1.0
F12 A:P9T403 4.8 34.6 0.8
O18 A:P9T403 4.8 31.8 0.8
CA A:ASN233 4.9 35.6 1.0
CZ A:PHE61 4.9 44.9 1.0
CE2 A:PHE61 4.9 45.0 1.0
N A:ASN233 5.0 35.7 1.0
CE1 A:PHE61 5.0 46.3 1.0

Fluorine binding site 3 out of 4 in 6dd0

Go back to Fluorine Binding Sites List in 6dd0
Fluorine binding site 3 out of 4 in the Crystal Structure of Vim-2 Complexed with Compound 8


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Vim-2 Complexed with Compound 8 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F403

b:31.7
occ:0.81
F12 B:P9T403 0.0 31.7 0.8
C11 B:P9T403 1.4 29.3 0.8
C13 B:P9T403 2.3 33.8 0.8
C10 B:P9T403 2.4 27.6 0.8
C05 B:P9T403 2.8 20.2 0.8
O B:HOH709 2.9 31.7 1.0
C04 B:P9T403 3.0 21.1 0.8
O B:HOH753 3.2 40.5 1.0
O07 B:P9T403 3.4 18.1 0.8
P06 B:P9T403 3.6 16.7 0.8
C14 B:P9T403 3.6 36.5 0.8
C17 B:P9T403 3.7 28.7 0.8
O B:HOH674 3.8 18.3 1.0
O09 B:P9T403 4.1 12.8 0.8
C16 B:P9T403 4.1 32.7 0.8
CE2 B:PHE61 4.2 36.6 1.0
CZ B:PHE61 4.3 37.1 1.0
CD2 B:PHE61 4.3 35.3 1.0
C03 B:P9T403 4.4 20.9 0.8
ND2 B:ASN233 4.4 38.1 1.0
CE1 B:PHE61 4.5 36.0 1.0
CG B:PHE61 4.6 33.8 1.0
CZ2 B:TRP87 4.6 16.6 1.0
CD1 B:PHE61 4.6 35.8 1.0
O B:HOH689 4.7 33.2 1.0
F15 B:P9T403 4.7 40.3 0.8
CB B:ASN233 4.8 32.9 1.0
O18 B:P9T403 4.9 28.3 0.8
CH2 B:TRP87 4.9 16.2 1.0
CG B:ASN233 4.9 35.6 1.0

Fluorine binding site 4 out of 4 in 6dd0

Go back to Fluorine Binding Sites List in 6dd0
Fluorine binding site 4 out of 4 in the Crystal Structure of Vim-2 Complexed with Compound 8


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Vim-2 Complexed with Compound 8 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F403

b:40.3
occ:0.81
F15 B:P9T403 0.0 40.3 0.8
C14 B:P9T403 1.4 36.5 0.8
C13 B:P9T403 2.4 33.8 0.8
C16 B:P9T403 2.4 32.7 0.8
CE1 B:PHE61 3.6 36.0 1.0
C11 B:P9T403 3.7 29.3 0.8
C17 B:P9T403 3.7 28.7 0.8
CD1 B:PHE61 3.7 35.8 1.0
CB B:ASN233 3.9 32.9 1.0
C10 B:P9T403 4.2 27.6 0.8
OH B:TYR67 4.5 29.1 1.0
CZ B:PHE61 4.7 37.1 1.0
OD2 B:ASP62 4.7 45.7 1.0
F12 B:P9T403 4.7 31.7 0.8
CG B:ASN233 4.7 35.6 1.0
O18 B:P9T403 4.8 28.3 0.8
CG B:PHE61 4.8 33.8 1.0
CA B:ASN233 4.9 31.7 1.0

Reference:

O.A.Pemberton, P.Jaishankar, A.Akhtar, J.L.Adams, L.N.Shaw, A.R.Renslo, Y.Chen. Heteroaryl Phosphonates As Noncovalent Inhibitors of Both Serine- and Metallocarbapenemases. J.Med.Chem. V. 62 8480 2019.
ISSN: ISSN 0022-2623
PubMed: 31483651
DOI: 10.1021/ACS.JMEDCHEM.9B00728
Page generated: Sun Dec 13 12:47:47 2020

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