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Fluorine in PDB 7pph: Crystal Structure of Nampt in Complex with Compound 10

Enzymatic activity of Crystal Structure of Nampt in Complex with Compound 10

All present enzymatic activity of Crystal Structure of Nampt in Complex with Compound 10:
2.4.2.12;

Protein crystallography data

The structure of Crystal Structure of Nampt in Complex with Compound 10, PDB code: 7pph was solved by R.C.Hillig, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.53 / 1.74
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 61.122, 105.778, 83.176, 90, 96.51, 90
R / Rfree (%) 19.5 / 22.9

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Nampt in Complex with Compound 10 (pdb code 7pph). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of Nampt in Complex with Compound 10, PDB code: 7pph:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 7pph

Go back to Fluorine Binding Sites List in 7pph
Fluorine binding site 1 out of 6 in the Crystal Structure of Nampt in Complex with Compound 10


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 Nampt in Complex with Compound 10 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:24.5
occ:1.00
 F17 A:7YE501 0.0 24.5 1.0
C15 A:7YE501 1.3 29.4 1.0
F18 A:7YE501 2.1 28.7 1.0
F16 A:7YE501 2.2 23.2 1.0
C14 A:7YE501 2.4 24.9 1.0
C20 A:7YE501 2.6 40.4 1.0
O13 A:7YE501 2.7 30.7 1.0
C19 A:7YE501 2.9 34.8 1.0
O A:HOH1031 2.9 24.9 1.0
C12 A:7YE501 2.9 34.1 1.0
O A:HOH931 3.1 33.6 1.0
O A:HOH861 3.3 25.9 1.0
C29 A:7YE501 3.7 26.9 1.0
C21 A:7YE501 3.8 50.8 1.0
CG A:ARG349 4.2 15.8 1.0
N11 A:7YE501 4.2 30.4 1.0
C28 A:7YE501 4.2 38.3 1.0
O A:HOH686 4.8 26.4 1.0
CB A:ARG349 4.8 14.9 1.0
CG A:PRO307 4.8 15.3 1.0
C9 A:7YE501 4.8 22.6 1.0
C22 A:7YE501 4.9 41.6 1.0
CD A:ARG349 4.9 15.8 1.0
N10 A:7YE501 4.9 19.5 1.0

Fluorine binding site 2 out of 6 in 7pph

Go back to Fluorine Binding Sites List in 7pph
Fluorine binding site 2 out of 6 in the Crystal Structure of Nampt in Complex with Compound 10


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 Nampt in Complex with Compound 10 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:28.7
occ:1.00
 F18 A:7YE501 0.0 28.7 1.0
C15 A:7YE501 1.3 29.4 1.0
F17 A:7YE501 2.1 24.5 1.0
F16 A:7YE501 2.2 23.2 1.0
C14 A:7YE501 2.3 24.9 1.0
C20 A:7YE501 2.7 40.4 1.0
C29 A:7YE501 2.8 26.9 1.0
C19 A:7YE501 2.8 34.8 1.0
CG1 A:ILE309 3.3 18.2 1.0
CD1 A:ILE309 3.4 17.6 1.0
C12 A:7YE501 3.6 34.1 1.0
CG A:PRO307 3.7 15.3 1.0
C21 A:7YE501 3.9 50.8 1.0
O A:HOH1031 4.0 24.9 1.0
O13 A:7YE501 4.1 30.7 1.0
C28 A:7YE501 4.1 38.3 1.0
C9 A:7YE501 4.1 22.6 1.0
CG A:ARG349 4.3 15.8 1.0
CB A:ARG349 4.3 14.9 1.0
CB A:ILE309 4.6 17.3 1.0
N11 A:7YE501 4.6 30.4 1.0
O A:HOH931 4.6 33.6 1.0
CB A:PRO307 4.7 15.7 1.0
CG2 A:ILE309 4.8 18.2 1.0
N10 A:7YE501 4.8 19.5 1.0
CD A:PRO307 4.8 15.7 1.0
C22 A:7YE501 4.9 41.6 1.0
C27 A:7YE501 4.9 31.1 1.0
CB A:PRO273 4.9 15.3 1.0
C23 A:7YE501 5.0 38.3 1.0

Fluorine binding site 3 out of 6 in 7pph

Go back to Fluorine Binding Sites List in 7pph
Fluorine binding site 3 out of 6 in the Crystal Structure of Nampt in Complex with Compound 10


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 Nampt in Complex with Compound 10 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:23.2
occ:1.00
 F16 A:7YE501 0.0 23.2 1.0
C15 A:7YE501 1.3 29.4 1.0
F17 A:7YE501 2.2 24.5 1.0
F18 A:7YE501 2.2 28.7 1.0
C14 A:7YE501 2.4 24.9 1.0
C12 A:7YE501 2.8 34.1 1.0
O A:HOH931 2.9 33.6 1.0
C29 A:7YE501 3.0 26.9 1.0
O13 A:7YE501 3.2 30.7 1.0
N11 A:7YE501 3.4 30.4 1.0
C9 A:7YE501 3.7 22.6 1.0
C19 A:7YE501 3.7 34.8 1.0
N10 A:7YE501 3.8 19.5 1.0
CB A:ALA379 3.8 13.0 1.0
C20 A:7YE501 4.0 40.4 1.0
CB A:ARG349 4.1 14.9 1.0
CG A:ARG349 4.2 15.8 1.0
CG1 A:ILE309 4.2 18.2 1.0
CG2 A:ILE309 4.5 18.2 1.0
O A:HOH861 4.7 25.9 1.0
C8 A:7YE501 4.8 19.9 1.0
CD1 A:ILE309 4.8 17.6 1.0
O A:HOH1031 4.9 24.9 1.0
C7 A:7YE501 4.9 21.9 1.0
C28 A:7YE501 4.9 38.3 1.0
CD A:ARG349 5.0 15.8 1.0
N A:ALA379 5.0 14.2 1.0

Fluorine binding site 4 out of 6 in 7pph

Go back to Fluorine Binding Sites List in 7pph
Fluorine binding site 4 out of 6 in the Crystal Structure of Nampt in Complex with Compound 10


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 Nampt in Complex with Compound 10 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:25.7
occ:1.00
 F17 B:7YE501 0.0 25.7 1.0
C15 B:7YE501 1.3 32.2 1.0
F18 B:7YE501 2.2 29.8 1.0
F16 B:7YE501 2.2 29.1 1.0
C14 B:7YE501 2.4 23.6 1.0
C20 B:7YE501 2.7 32.8 1.0
O13 B:7YE501 2.8 30.3 1.0
O B:HOH1020 2.8 20.5 1.0
C19 B:7YE501 2.9 24.4 1.0
C12 B:7YE501 2.9 27.2 1.0
O B:HOH951 3.4 24.1 1.0
O B:HOH913 3.5 46.2 1.0
C29 B:7YE501 3.7 23.8 1.0
C21 B:7YE501 3.9 32.2 1.0
CG B:ARG349 4.2 13.1 1.0
N11 B:7YE501 4.2 22.4 1.0
C28 B:7YE501 4.3 29.3 1.0
CG B:PRO307 4.6 14.4 1.0
CB B:ARG349 4.8 12.4 1.0
C9 B:7YE501 4.8 23.9 1.0
O B:HOH722 4.8 32.2 1.0
N10 B:7YE501 4.9 21.6 1.0
CD B:ARG349 5.0 14.4 1.0

Fluorine binding site 5 out of 6 in 7pph

Go back to Fluorine Binding Sites List in 7pph
Fluorine binding site 5 out of 6 in the Crystal Structure of Nampt in Complex with Compound 10


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Nampt in Complex with Compound 10 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:29.8
occ:1.00
 F18 B:7YE501 0.0 29.8 1.0
C15 B:7YE501 1.3 32.2 1.0
F17 B:7YE501 2.2 25.7 1.0
F16 B:7YE501 2.2 29.1 1.0
C14 B:7YE501 2.4 23.6 1.0
C29 B:7YE501 2.7 23.8 1.0
C20 B:7YE501 3.0 32.8 1.0
C19 B:7YE501 3.1 24.4 1.0
CG1 B:ILE309 3.1 13.9 1.0
CD1 B:ILE309 3.2 13.5 1.0
C12 B:7YE501 3.6 27.2 1.0
CG B:PRO307 3.7 14.4 1.0
C9 B:7YE501 4.0 23.9 1.0
O B:HOH1020 4.2 20.5 1.0
O13 B:7YE501 4.2 30.3 1.0
CB B:ARG349 4.2 12.4 1.0
CG B:ARG349 4.3 13.1 1.0
C21 B:7YE501 4.3 32.2 1.0
C28 B:7YE501 4.4 29.3 1.0
CB B:ILE309 4.5 13.8 1.0
N11 B:7YE501 4.6 22.4 1.0
CG2 B:ILE309 4.7 13.5 1.0
N10 B:7YE501 4.7 21.6 1.0
CB B:PRO307 4.7 14.7 1.0
O B:HOH913 4.7 46.2 1.0
CD B:PRO307 4.9 15.4 1.0
C8 B:7YE501 4.9 16.7 1.0
CB B:PRO273 5.0 15.9 1.0
C7 B:7YE501 5.0 20.7 1.0

Fluorine binding site 6 out of 6 in 7pph

Go back to Fluorine Binding Sites List in 7pph
Fluorine binding site 6 out of 6 in the Crystal Structure of Nampt in Complex with Compound 10


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Nampt in Complex with Compound 10 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:29.1
occ:1.00
 F16 B:7YE501 0.0 29.1 1.0
C15 B:7YE501 1.3 32.2 1.0
F18 B:7YE501 2.2 29.8 1.0
F17 B:7YE501 2.2 25.7 1.0
C14 B:7YE501 2.4 23.6 1.0
C12 B:7YE501 2.7 27.2 1.0
O B:HOH913 2.7 46.2 1.0
C29 B:7YE501 3.0 23.8 1.0
O13 B:7YE501 3.2 30.3 1.0
N11 B:7YE501 3.4 22.4 1.0
C9 B:7YE501 3.6 23.9 1.0
N10 B:7YE501 3.7 21.6 1.0
C19 B:7YE501 3.8 24.4 1.0
CB B:ALA379 3.9 14.4 1.0
CB B:ARG349 4.1 12.4 1.0
C20 B:7YE501 4.2 32.8 1.0
CG B:ARG349 4.3 13.1 1.0
CG1 B:ILE309 4.3 13.9 1.0
O B:HOH951 4.7 24.1 1.0
CG2 B:ILE309 4.7 13.5 1.0
C8 B:7YE501 4.7 16.7 1.0
CD1 B:ILE309 4.8 13.5 1.0
O B:HOH1020 4.8 20.5 1.0
C7 B:7YE501 4.9 20.7 1.0
O B:HOH722 4.9 32.2 1.0
CD B:ARG349 5.0 14.4 1.0

Reference:

N.Bohnke, M.Berger, N.Griebenow, A.Rottmann, M.Erkelenz, S.Hammer, S.Berndt, J.Gunther, A.M.Wengner, B.Stelte-Ludwig, C.Mahlert, S.Greven, L.Dietz, H.Jorissen, N.Barak, U.Bomer, R.C.Hillig, U.Eberspaecher, J.Weiske, A.Giese, D.Mumberg, C.F.Nising, H.Weinmann, A.Sommer. A Novel Nampt Inhibitor-Based Antibody-Drug Conjugate Payload Class For Cancer Therapy. Bioconjug.Chem. V. 33 1210 2022.
ISSN: ISSN 1043-1802
PubMed: 35658441
DOI: 10.1021/ACS.BIOCONJCHEM.2C00178
Page generated: Fri Aug 2 11:08:16 2024

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