Fluorine in PDB 8d0c: Human SARM1 Tir Domain Bound to Nb-3-Adpr

All present enzymatic activity of Human SARM1 Tir Domain Bound to Nb-3-Adpr:
3.2.2.6;

The structure of Human SARM1 Tir Domain Bound to Nb-3-Adpr, PDB code: 8d0c was solved by M.A.Bratkowski, P.Mathur, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	69.91 / 2.09
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	87.086, 117.23, 32.865, 90, 90, 90
R / Rfree (%)	17.6 / 22.3

The binding sites of Fluorine atom in the Human SARM1 Tir Domain Bound to Nb-3-Adpr (pdb code 8d0c). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Human SARM1 Tir Domain Bound to Nb-3-Adpr, PDB code: 8d0c:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the Human SARM1 Tir Domain Bound to Nb-3-Adpr


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Human SARM1 Tir Domain Bound to Nb-3-Adpr within 5.0Å range: probe atom residue distance (Å) B Occ A:F801 b:31.6 occ:1.00 F49 A:Q1F801 0.0 31.6 1.0 C48 A:Q1F801 1.4 31.1 1.0 F50 A:Q1F801 2.2 27.4 1.0 F51 A:Q1F801 2.2 35.5 1.0 C47 A:Q1F801 2.3 31.2 1.0 NH2 A:ARG570 2.8 33.3 1.0 N46 A:Q1F801 2.8 27.9 1.0 O52 A:Q1F801 3.1 32.2 1.0 C45 A:Q1F801 3.2 31.1 1.0 CB A:ASP594 3.6 25.4 1.0 CG A:ASP594 3.7 29.9 1.0 OD2 A:ASP594 3.7 26.8 1.0 C A:ASP594 3.8 30.9 1.0 O A:ASP594 3.9 31.5 1.0 N A:VAL595 3.9 29.3 1.0 CG1 A:VAL595 4.0 28.1 1.0 CZ A:ARG570 4.0 36.7 1.0 CA A:VAL595 4.1 34.0 1.0 OD1 A:ASP594 4.3 27.3 1.0 C04 A:Q1F801 4.3 31.2 1.0 CA A:ASP594 4.4 26.4 1.0 N44 A:Q1F801 4.4 29.2 1.0 CD2 A:LEU598 4.4 26.9 1.0 NH1 A:ARG570 4.7 41.5 1.0 CB A:VAL595 4.7 32.6 1.0 O A:HOH902 4.7 33.2 1.0 NE A:ARG570 4.8 40.1 1.0 CB A:LEU598 4.8 27.5 1.0 C05 A:Q1F801 4.9 28.6 1.0

Fluorine binding site 2 out of 6 in the Human SARM1 Tir Domain Bound to Nb-3-Adpr


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Human SARM1 Tir Domain Bound to Nb-3-Adpr within 5.0Å range: probe atom residue distance (Å) B Occ A:F801 b:27.4 occ:1.00 F50 A:Q1F801 0.0 27.4 1.0 C48 A:Q1F801 1.4 31.1 1.0 F49 A:Q1F801 2.2 31.6 1.0 F51 A:Q1F801 2.2 35.5 1.0 C47 A:Q1F801 2.4 31.2 1.0 N46 A:Q1F801 2.8 27.9 1.0 O A:HOH902 3.2 33.2 1.0 O A:ASP594 3.5 31.5 1.0 CD2 A:LEU598 3.6 26.9 1.0 CB A:LEU598 3.7 27.5 1.0 O A:LEU598 3.7 30.6 1.0 C45 A:Q1F801 3.9 31.1 1.0 CG A:LEU598 4.0 26.6 1.0 C A:ASP594 4.2 30.9 1.0 O52 A:Q1F801 4.4 32.2 1.0 C A:LEU598 4.5 30.5 1.0 CA A:LEU598 4.6 27.2 1.0 CA A:VAL595 4.6 34.0 1.0 CB A:ASP594 4.7 25.4 1.0 N A:VAL595 4.7 29.3 1.0 N44 A:Q1F801 4.9 29.2 1.0 CA A:ASP594 4.9 26.4 1.0 NH2 A:ARG570 5.0 33.3 1.0

Fluorine binding site 3 out of 6 in the Human SARM1 Tir Domain Bound to Nb-3-Adpr


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Human SARM1 Tir Domain Bound to Nb-3-Adpr within 5.0Å range: probe atom residue distance (Å) B Occ A:F801 b:35.5 occ:1.00 F51 A:Q1F801 0.0 35.5 1.0 C48 A:Q1F801 1.4 31.1 1.0 F50 A:Q1F801 2.2 27.4 1.0 F49 A:Q1F801 2.2 31.6 1.0 C47 A:Q1F801 2.3 31.2 1.0 CA A:VAL595 3.5 34.0 1.0 O A:HOH902 3.5 33.2 1.0 N46 A:Q1F801 3.6 27.9 1.0 CG1 A:VAL595 3.7 28.1 1.0 O A:ASP594 4.0 31.5 1.0 O A:HOH903 4.0 34.1 1.0 CB A:VAL595 4.1 32.6 1.0 N A:VAL595 4.1 29.3 1.0 O B:HOH972 4.3 37.6 1.0 C A:ASP594 4.3 30.9 1.0 C A:VAL595 4.4 31.3 1.0 O A:VAL595 4.4 37.0 1.0 O52 A:Q1F801 4.6 32.2 1.0 C45 A:Q1F801 4.6 31.1 1.0 NH2 A:ARG570 4.6 33.3 1.0 CG B:GLU686 5.0 39.7 1.0

Fluorine binding site 4 out of 6 in the Human SARM1 Tir Domain Bound to Nb-3-Adpr


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Human SARM1 Tir Domain Bound to Nb-3-Adpr within 5.0Å range: probe atom residue distance (Å) B Occ B:F801 b:36.3 occ:1.00 F49 B:Q1F801 0.0 36.3 1.0 C48 B:Q1F801 1.4 29.8 1.0 F51 B:Q1F801 2.2 30.4 1.0 F50 B:Q1F801 2.2 33.9 1.0 C47 B:Q1F801 2.3 34.6 1.0 O B:HOH911 3.4 34.1 1.0 CA B:VAL595 3.5 34.9 1.0 N46 B:Q1F801 3.6 28.4 1.0 O B:ASP594 3.8 30.1 1.0 CG1 B:VAL595 3.9 31.7 1.0 O A:HOH945 3.9 41.1 1.0 N B:VAL595 4.1 32.5 1.0 C B:ASP594 4.2 33.9 1.0 CB B:VAL595 4.2 33.6 1.0 C B:VAL595 4.3 36.6 1.0 O B:VAL595 4.3 41.8 1.0 O52 B:Q1F801 4.5 31.2 1.0 C45 B:Q1F801 4.6 30.1 1.0 NH2 B:ARG570 4.6 35.8 1.0 CG A:GLU686 4.7 38.5 1.0 O B:HOH938 5.0 41.0 1.0

Fluorine binding site 5 out of 6 in the Human SARM1 Tir Domain Bound to Nb-3-Adpr


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Human SARM1 Tir Domain Bound to Nb-3-Adpr within 5.0Å range: probe atom residue distance (Å) B Occ B:F801 b:33.9 occ:1.00 F50 B:Q1F801 0.0 33.9 1.0 C48 B:Q1F801 1.4 29.8 1.0 F51 B:Q1F801 2.2 30.4 1.0 F49 B:Q1F801 2.2 36.3 1.0 C47 B:Q1F801 2.3 34.6 1.0 N46 B:Q1F801 2.8 28.4 1.0 NH2 B:ARG570 3.0 35.8 1.0 O52 B:Q1F801 3.1 31.2 1.0 C45 B:Q1F801 3.2 30.1 1.0 CB B:ASP594 3.6 27.3 1.0 CG B:ASP594 3.7 32.9 1.0 OD2 B:ASP594 3.8 31.5 1.0 C B:ASP594 3.8 33.9 1.0 O B:ASP594 3.8 30.1 1.0 N B:VAL595 4.0 32.5 1.0 CZ B:ARG570 4.1 41.3 1.0 CA B:VAL595 4.2 34.9 1.0 CA B:ASP594 4.3 28.1 1.0 C43 B:Q1F801 4.3 27.5 1.0 CD2 B:LEU598 4.3 26.1 1.0 CG1 B:VAL595 4.3 31.7 1.0 OD1 B:ASP594 4.4 30.7 1.0 N44 B:Q1F801 4.4 29.9 1.0 O B:HOH911 4.6 34.1 1.0 O B:HOH938 4.7 41.0 1.0 CB B:LEU598 4.8 28.2 1.0 NH1 B:ARG570 4.8 42.3 1.0 O A:HOH945 4.8 41.1 1.0 C42 B:Q1F801 4.9 30.4 1.0 CB B:VAL595 4.9 33.6 1.0 NE B:ARG570 5.0 43.6 1.0

Fluorine binding site 6 out of 6 in the Human SARM1 Tir Domain Bound to Nb-3-Adpr


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Human SARM1 Tir Domain Bound to Nb-3-Adpr within 5.0Å range: probe atom residue distance (Å) B Occ B:F801 b:30.4 occ:1.00 F51 B:Q1F801 0.0 30.4 1.0 C48 B:Q1F801 1.4 29.8 1.0 F50 B:Q1F801 2.2 33.9 1.0 F49 B:Q1F801 2.2 36.3 1.0 C47 B:Q1F801 2.4 34.6 1.0 N46 B:Q1F801 2.8 28.4 1.0 O B:HOH911 3.1 34.1 1.0 O B:ASP594 3.5 30.1 1.0 CD2 B:LEU598 3.6 26.1 1.0 CB B:LEU598 3.6 28.2 1.0 O B:LEU598 3.7 32.7 1.0 CG B:LEU598 3.9 27.2 1.0 C45 B:Q1F801 4.0 30.1 1.0 C B:ASP594 4.1 33.9 1.0 C B:LEU598 4.5 31.3 1.0 O52 B:Q1F801 4.5 31.2 1.0 CA B:LEU598 4.6 28.6 1.0 CA B:VAL595 4.6 34.9 1.0 CB B:ASP594 4.7 27.3 1.0 N B:VAL595 4.7 32.5 1.0 CA B:ASP594 4.9 28.1 1.0 N B:LEU598 5.0 28.5 1.0

M.Bratkowski, T.C.Burdett, J.Danao, X.Wang, P.Mathur, W.Gu, J.A.Beckstead, S.Talreja, Y.S.Yang, G.Danko, J.H.Park, M.Walton, S.P.Brown, C.M.Tegley, P.R.B.Joseph, C.H.Reynolds, S.Sambashivan. Uncompetitive, Adduct-Forming SARM1 Inhibitors Are Neuroprotective in Preclinical Models of Nerve Injury and Disease. Neuron V. 110 3711 2022.
ISSN: ISSN 0896-6273
PubMed: 36087583
DOI: 10.1016/J.NEURON.2022.08.017