Fluorine in PDB 8d0h: Human SARM1 Tir Domain Bound to Nb-3-Gdpr

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

The structure of Human SARM1 Tir Domain Bound to Nb-3-Gdpr, PDB code: 8d0h 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)	46.54 / 2.37
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	33.048, 77.707, 116.227, 90, 90, 90
R / Rfree (%)	19.3 / 28.1

The binding sites of Fluorine atom in the Human SARM1 Tir Domain Bound to Nb-3-Gdpr (pdb code 8d0h). 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-Gdpr, PDB code: 8d0h:
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-Gdpr


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-Gdpr within 5.0Å range: probe atom residue distance (Å) B Occ A:F801 b:41.5 occ:1.00 F49 A:Q1O801 0.0 41.5 1.0 C48 A:Q1O801 1.4 31.6 1.0 F50 A:Q1O801 2.2 32.7 1.0 F51 A:Q1O801 2.2 39.0 1.0 C47 A:Q1O801 2.4 35.0 1.0 N46 A:Q1O801 2.9 36.6 1.0 O52 A:Q1O801 3.0 44.0 1.0 C45 A:Q1O801 3.2 41.6 1.0 CB A:ASP594 3.4 24.9 1.0 CG A:ASP594 3.6 31.1 1.0 C A:ASP594 3.7 36.0 1.0 OD2 A:ASP594 3.7 34.3 1.0 N A:VAL595 3.8 36.0 1.0 NH2 A:ARG570 3.8 44.8 1.0 O A:ASP594 3.9 28.6 1.0 CA A:VAL595 4.0 31.2 1.0 CD2 A:LEU598 4.1 30.6 1.0 C41 A:Q1O801 4.1 39.7 1.0 CG1 A:VAL595 4.1 31.1 1.0 CA A:ASP594 4.1 26.9 1.0 N44 A:Q1O801 4.4 38.3 1.0 OD1 A:ASP594 4.4 29.0 1.0 CB A:LEU598 4.4 20.9 1.0 C40 A:Q1O801 4.5 38.9 1.0 CZ A:ARG570 4.7 41.0 1.0 CB A:VAL595 4.8 26.6 1.0 CG A:LEU598 4.8 25.7 1.0 C42 A:Q1O801 5.0 35.6 1.0

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


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-Gdpr within 5.0Å range: probe atom residue distance (Å) B Occ A:F801 b:32.7 occ:1.00 F50 A:Q1O801 0.0 32.7 1.0 C48 A:Q1O801 1.4 31.6 1.0 F49 A:Q1O801 2.2 41.5 1.0 F51 A:Q1O801 2.2 39.0 1.0 C47 A:Q1O801 2.4 35.0 1.0 CA A:VAL595 3.1 31.2 1.0 CG1 A:VAL595 3.5 31.1 1.0 N46 A:Q1O801 3.7 36.6 1.0 N A:VAL595 3.7 36.0 1.0 O A:ASP594 3.7 28.6 1.0 CB A:VAL595 3.8 26.6 1.0 C A:ASP594 3.9 36.0 1.0 C A:VAL595 4.0 38.0 1.0 O A:VAL595 4.2 46.0 1.0 O52 A:Q1O801 4.5 44.0 1.0 C45 A:Q1O801 4.6 41.6 1.0 N25 A:Q1O801 4.7 35.3 1.0 O A:LEU598 4.8 33.7 1.0 CG B:GLU686 4.9 25.9 1.0 CB A:ASP594 4.9 24.9 1.0

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


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-Gdpr within 5.0Å range: probe atom residue distance (Å) B Occ A:F801 b:39.0 occ:1.00 F51 A:Q1O801 0.0 39.0 1.0 C48 A:Q1O801 1.4 31.6 1.0 F49 A:Q1O801 2.2 41.5 1.0 F50 A:Q1O801 2.2 32.7 1.0 C47 A:Q1O801 2.4 35.0 1.0 N46 A:Q1O801 2.9 36.6 1.0 O A:LEU598 3.4 33.7 1.0 CD2 A:LEU598 3.4 30.6 1.0 CB A:LEU598 3.4 20.9 1.0 O A:ASP594 3.6 28.6 1.0 CG A:LEU598 3.7 25.7 1.0 C45 A:Q1O801 4.0 41.6 1.0 C A:ASP594 4.2 36.0 1.0 C A:LEU598 4.2 36.1 1.0 CA A:LEU598 4.4 26.3 1.0 O52 A:Q1O801 4.4 44.0 1.0 CA A:VAL595 4.6 31.2 1.0 N A:VAL595 4.6 36.0 1.0 CB A:ASP594 4.7 24.9 1.0 CA A:ASP594 4.9 26.9 1.0 N A:LEU598 4.9 32.6 1.0 N44 A:Q1O801 5.0 38.3 1.0

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


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-Gdpr within 5.0Å range: probe atom residue distance (Å) B Occ B:F801 b:33.3 occ:1.00 F49 B:Q1O801 0.0 33.3 1.0 C48 B:Q1O801 1.4 33.7 1.0 F50 B:Q1O801 2.2 42.1 1.0 F51 B:Q1O801 2.2 31.3 1.0 C47 B:Q1O801 2.4 35.5 1.0 N46 B:Q1O801 2.7 43.9 1.0 NH2 B:ARG570 2.9 43.7 1.0 O52 B:Q1O801 2.9 41.6 1.0 C45 B:Q1O801 3.0 42.9 1.0 OD2 B:ASP594 3.3 29.5 1.0 CB B:ASP594 3.5 28.2 1.0 CG B:ASP594 3.5 29.8 1.0 C B:ASP594 3.8 27.9 1.0 O B:ASP594 3.8 27.5 1.0 C41 B:Q1O801 3.9 32.2 1.0 N B:VAL595 4.1 28.7 1.0 N44 B:Q1O801 4.2 37.9 1.0 CZ B:ARG570 4.2 46.1 1.0 CD2 B:LEU598 4.2 31.9 1.0 CA B:ASP594 4.2 30.0 1.0 OD1 B:ASP594 4.3 30.7 1.0 CA B:VAL595 4.3 31.3 1.0 CB B:LEU598 4.5 26.0 1.0 C40 B:Q1O801 4.5 33.4 1.0 CG1 B:VAL595 4.6 35.1 1.0 NE B:ARG570 4.8 46.3 1.0 C42 B:Q1O801 4.8 31.4 1.0 CG B:LEU598 4.9 37.8 1.0 C53 B:Q1O801 4.9 33.6 1.0

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


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-Gdpr within 5.0Å range: probe atom residue distance (Å) B Occ B:F801 b:42.1 occ:1.00 F50 B:Q1O801 0.0 42.1 1.0 C48 B:Q1O801 1.4 33.7 1.0 F49 B:Q1O801 2.2 33.3 1.0 F51 B:Q1O801 2.2 31.3 1.0 C47 B:Q1O801 2.4 35.5 1.0 CA B:VAL595 3.3 31.3 1.0 CG1 B:VAL595 3.6 35.1 1.0 N46 B:Q1O801 3.7 43.9 1.0 O B:ASP594 3.8 27.5 1.0 N B:VAL595 3.8 28.7 1.0 NH2 B:ARG570 3.9 43.7 1.0 C B:ASP594 4.0 27.9 1.0 CB B:VAL595 4.0 35.0 1.0 OE1 A:GLU686 4.1 58.7 1.0 O B:VAL595 4.1 41.5 1.0 C B:VAL595 4.2 35.4 1.0 O52 B:Q1O801 4.3 41.6 1.0 O A:HOH904 4.3 34.0 1.0 CD A:GLU686 4.4 55.0 1.0 C45 B:Q1O801 4.4 42.9 1.0 OE2 A:GLU686 4.5 63.2 1.0 CG B:ASP594 4.8 29.8 1.0 OD2 B:ASP594 4.8 29.5 1.0 CB B:ASP594 4.9 28.2 1.0 CZ B:ARG570 5.0 46.1 1.0 N25 B:Q1O801 5.0 46.1 1.0

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


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-Gdpr within 5.0Å range: probe atom residue distance (Å) B Occ B:F801 b:31.3 occ:1.00 F51 B:Q1O801 0.0 31.3 1.0 C48 B:Q1O801 1.4 33.7 1.0 F49 B:Q1O801 2.2 33.3 1.0 F50 B:Q1O801 2.2 42.1 1.0 C47 B:Q1O801 2.4 35.5 1.0 N46 B:Q1O801 3.0 43.9 1.0 O B:ASP594 3.3 27.5 1.0 CB B:LEU598 3.5 26.0 1.0 O B:LEU598 3.9 39.0 1.0 CD2 B:LEU598 3.9 31.9 1.0 C B:ASP594 4.0 27.9 1.0 CG B:LEU598 4.0 37.8 1.0 C45 B:Q1O801 4.1 42.9 1.0 CA B:VAL595 4.4 31.3 1.0 C B:LEU598 4.4 37.0 1.0 CA B:LEU598 4.4 28.1 1.0 O52 B:Q1O801 4.5 41.6 1.0 N B:VAL595 4.5 28.7 1.0 CB B:ASP594 4.6 28.2 1.0 CA B:ASP594 4.8 30.0 1.0 O B:VAL595 4.8 41.5 1.0 N B:LEU598 4.9 33.3 1.0 C B:VAL595 4.9 35.4 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