Fluorine in PDB 5knj: Pseudokinase Domain of Mlkl Bound to Compound 1.

The structure of Pseudokinase Domain of Mlkl Bound to Compound 1., PDB code: 5knj was solved by D.J.Marcotte, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	71.45 / 2.88
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.488, 90.879, 115.618, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 25.6

The binding sites of Fluorine atom in the Pseudokinase Domain of Mlkl Bound to Compound 1. (pdb code 5knj). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Pseudokinase Domain of Mlkl Bound to Compound 1., PDB code: 5knj:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the Pseudokinase Domain of Mlkl Bound to Compound 1.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Pseudokinase Domain of Mlkl Bound to Compound 1. within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:49.6 occ:1.00 F1 A:6UX501 0.0 49.6 1.0 C1 A:6UX501 0.7 48.1 1.0 F3 A:6UX501 1.1 48.7 1.0 F2 A:6UX501 1.2 46.2 1.0 OH A:6UX501 1.7 50.0 1.0 CZ A:6UX501 3.0 46.1 1.0 CE2 A:6UX501 3.8 46.8 1.0 CE1 A:6UX501 3.8 48.2 1.0 CD1 A:LEU320 3.9 28.9 1.0 CG2 A:THR253 4.0 33.7 1.0 CD2 A:LEU320 4.1 28.6 1.0 CG2 A:ILE262 4.3 24.2 1.0 CD2 A:PHE257 4.4 33.0 1.0 CG A:LEU320 4.4 28.3 1.0 CB A:PHE257 4.4 35.3 1.0 CD1 A:ILE262 4.6 24.4 1.0 CG A:PHE257 4.7 33.7 1.0 O A:THR253 4.8 37.7 1.0

Fluorine binding site 2 out of 6 in the Pseudokinase Domain of Mlkl Bound to Compound 1.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Pseudokinase Domain of Mlkl Bound to Compound 1. within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:46.2 occ:1.00 F2 A:6UX501 0.0 46.2 1.0 C1 A:6UX501 0.8 48.1 1.0 F1 A:6UX501 1.2 49.6 1.0 F3 A:6UX501 1.3 48.7 1.0 OH A:6UX501 1.9 50.0 1.0 CZ A:6UX501 2.7 46.1 1.0 CE2 A:6UX501 3.3 46.8 1.0 CE1 A:6UX501 3.5 48.2 1.0 O A:LEU347 4.3 33.4 1.0 CD2 A:LEU320 4.3 28.6 1.0 CD2 A:HIS329 4.4 45.3 1.0 CD2 A:6UX501 4.5 48.2 1.0 CG2 A:ILE262 4.5 24.2 1.0 CD1 A:LEU320 4.5 28.9 1.0 CG A:LEU347 4.5 33.2 1.0 CD1 A:6UX501 4.7 49.8 1.0 C A:LEU347 4.7 33.6 1.0 CD1 A:ILE262 4.7 24.4 1.0 C A:ALA348 4.7 43.8 1.0 CA A:ALA348 4.8 40.6 1.0 NE2 A:HIS329 4.8 47.5 1.0 CG2 A:THR253 4.8 33.7 1.0 CD2 A:LEU347 4.9 32.9 1.0 N A:ALA348 4.9 37.3 1.0 CG A:LEU320 5.0 28.3 1.0 N A:GLY349 5.0 51.9 1.0

Fluorine binding site 3 out of 6 in the Pseudokinase Domain of Mlkl Bound to Compound 1.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Pseudokinase Domain of Mlkl Bound to Compound 1. within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:48.7 occ:1.00 F3 A:6UX501 0.0 48.7 1.0 C1 A:6UX501 0.7 48.1 1.0 F1 A:6UX501 1.1 49.6 1.0 F2 A:6UX501 1.3 46.2 1.0 OH A:6UX501 1.8 50.0 1.0 CZ A:6UX501 2.7 46.1 1.0 CE1 A:6UX501 3.2 48.2 1.0 CG2 A:THR253 3.6 33.7 1.0 CE2 A:6UX501 3.7 46.8 1.0 CD2 A:LEU320 4.3 28.6 1.0 CD1 A:6UX501 4.5 49.8 1.0 CD1 A:LEU320 4.7 28.9 1.0 CD2 A:HIS329 4.7 45.3 1.0 CG A:LEU320 4.8 28.3 1.0 CD2 A:6UX501 4.9 48.2 1.0 CD2 A:PHE257 4.9 33.0 1.0 CB A:THR253 4.9 34.4 1.0

Fluorine binding site 4 out of 6 in the Pseudokinase Domain of Mlkl Bound to Compound 1.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Pseudokinase Domain of Mlkl Bound to Compound 1. within 5.0Å range: probe atom residue distance (Å) B Occ B:F501 b:39.5 occ:1.00 F1 B:6UX501 0.0 39.5 1.0 C1 B:6UX501 1.3 37.6 1.0 F3 B:6UX501 2.2 41.0 1.0 F2 B:6UX501 2.2 39.2 1.0 OH B:6UX501 2.3 36.6 1.0 CZ B:6UX501 2.7 35.0 1.0 CE1 B:6UX501 3.2 33.2 1.0 O B:LEU347 3.3 37.4 1.0 CE2 B:6UX501 3.5 34.2 1.0 C B:LEU347 3.8 34.7 1.0 CA B:ALA348 4.0 35.9 1.0 N B:ALA348 4.1 35.2 1.0 CG B:LEU347 4.1 33.0 1.0 CG2 B:ILE262 4.1 28.9 1.0 C B:ALA348 4.2 37.3 1.0 CD1 B:6UX501 4.3 33.2 1.0 CB B:LEU347 4.4 31.6 1.0 CD2 B:HIS329 4.4 40.2 1.0 CD1 B:ILE262 4.4 30.0 1.0 CD2 B:6UX501 4.5 32.8 1.0 N B:GLY349 4.5 41.6 1.0 O B:ALA348 4.6 36.2 1.0 NE2 B:HIS329 4.7 39.5 1.0 CD2 B:LEU347 4.7 34.9 1.0 CA B:LEU347 4.7 31.9 1.0 CG B:6UX501 4.8 32.9 1.0 CD2 B:LEU320 4.9 40.9 1.0

Fluorine binding site 5 out of 6 in the Pseudokinase Domain of Mlkl Bound to Compound 1.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Pseudokinase Domain of Mlkl Bound to Compound 1. within 5.0Å range: probe atom residue distance (Å) B Occ B:F501 b:39.2 occ:1.00 F2 B:6UX501 0.0 39.2 1.0 C1 B:6UX501 1.3 37.6 1.0 F3 B:6UX501 2.2 41.0 1.0 F1 B:6UX501 2.2 39.5 1.0 OH B:6UX501 2.3 36.6 1.0 CZ B:6UX501 2.7 35.0 1.0 CE2 B:6UX501 2.7 34.2 1.0 CE1 B:6UX501 3.9 33.2 1.0 CD2 B:6UX501 3.9 32.8 1.0 CD2 B:HIS329 3.9 40.2 1.0 CG2 B:THR253 4.3 30.1 1.0 NE2 B:HIS329 4.3 39.5 1.0 CD2 B:LEU320 4.6 40.9 1.0 N B:GLY349 4.6 41.6 1.0 CA B:GLY349 4.7 43.1 1.0 C B:ALA348 4.8 37.3 1.0 CD1 B:6UX501 4.8 33.2 1.0 CG B:6UX501 4.8 32.9 1.0 CG B:HIS329 4.9 38.5 1.0 O B:ALA348 5.0 36.2 1.0

Fluorine binding site 6 out of 6 in the Pseudokinase Domain of Mlkl Bound to Compound 1.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Pseudokinase Domain of Mlkl Bound to Compound 1. within 5.0Å range: probe atom residue distance (Å) B Occ B:F501 b:41.0 occ:1.00 F3 B:6UX501 0.0 41.0 1.0 C1 B:6UX501 1.3 37.6 1.0 F1 B:6UX501 2.2 39.5 1.0 F2 B:6UX501 2.2 39.2 1.0 OH B:6UX501 2.2 36.6 1.0 CZ B:6UX501 3.5 35.0 1.0 CD1 B:LEU320 3.5 41.8 1.0 CD2 B:LEU320 3.6 40.9 1.0 CG B:LEU320 3.9 40.0 1.0 CG2 B:THR253 4.1 30.1 1.0 CE2 B:6UX501 4.2 34.2 1.0 CD2 B:PHE257 4.4 39.7 1.0 CE1 B:6UX501 4.4 33.2 1.0 CG2 B:ILE262 4.4 28.9 1.0 CD1 B:ILE262 4.4 30.0 1.0 CB B:PHE257 4.5 34.8 1.0 CG B:PHE257 4.7 37.5 1.0 CD2 B:HIS329 4.9 40.2 1.0

B.Ma, D.Marcotte, M.Paramasivam, K.Michelsen, T.Wang, A.Bertolotti-Ciarlet, J.H.Jones, B.Moree, M.Butko, J.Salafsky, X.Sun, T.Mckee, L.F.Silvian. Atp-Competitive Mlkl Binders Have No Functional Impact on Necroptosis. Plos One V. 11 65983 2016.
ISSN: ESSN 1932-6203
PubMed: 27832137
DOI: 10.1371/JOURNAL.PONE.0165983