Chlorine in PDB 8v2f: Crystal Structure of IRAK4 Kinase Domain with Compound 9

All present enzymatic activity of Crystal Structure of IRAK4 Kinase Domain with Compound 9:
2.7.11.1;

The structure of Crystal Structure of IRAK4 Kinase Domain with Compound 9, PDB code: 8v2f was solved by M.M.Weiss, X.Zheng, C.M.Browne, V.Campbell, D.Chen, B.Enerson, X.Fei, X.Huang, C.R.Klaus, H.Li, M.Mayo, A.A.Mcdonald, A.Paul, K.Sharma, Y.Shi, A.Slavin, D.M.Walter, K.Yuan, Y.Zhang, X.Zhu, J.Kelleher, N.Ji, D.Walker, N.Mainolfi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.14 / 2.09
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	142.87, 140.68, 89.02, 90, 124, 90
R / Rfree (%)	16.8 / 20.8

The structure of Crystal Structure of IRAK4 Kinase Domain with Compound 9 also contains other interesting chemical elements:

Fluorine

(F)

12 atoms

The binding sites of Chlorine atom in the Crystal Structure of IRAK4 Kinase Domain with Compound 9 (pdb code 8v2f). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Crystal Structure of IRAK4 Kinase Domain with Compound 9, PDB code: 8v2f:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Crystal Structure of IRAK4 Kinase Domain with Compound 9


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of IRAK4 Kinase Domain with Compound 9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl502 b:69.2 occ:1.00 O A:HOH731 2.6 48.9 1.0 O A:GLY350 3.5 31.4 1.0 O A:ILE348 4.0 42.5 1.0 N A:GLY350 4.3 36.4 1.0 OG1 A:THR352 4.3 31.4 1.0 SD A:MET355 4.3 35.1 1.0 C A:GLY350 4.4 35.8 1.0 C A:VAL349 4.4 40.4 1.0 CA A:VAL349 4.5 44.4 1.0 CG2 A:ILE348 4.6 41.6 1.0 C A:ILE348 4.6 36.1 1.0 CE A:MET355 4.8 33.6 1.0 N A:VAL349 4.8 43.9 1.0 CA A:GLY350 4.9 39.2 1.0

Chlorine binding site 2 out of 3 in the Crystal Structure of IRAK4 Kinase Domain with Compound 9


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of IRAK4 Kinase Domain with Compound 9 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl502 b:84.5 occ:1.00 O B:HOH614 3.5 41.3 1.0 CD1 B:TRP285 4.0 32.2 1.0 CA B:HIS286 4.2 30.6 1.0 ND1 B:HIS286 4.2 34.7 1.0 SG B:CYS289 4.4 32.3 1.0 NE1 B:TRP285 4.5 31.4 1.0 CB B:HIS286 4.5 29.0 1.0 N B:HIS286 4.5 29.7 1.0 CB B:CYS289 4.9 30.9 1.0 CG B:HIS286 4.9 31.9 1.0 CG2 B:THR458 4.9 53.6 1.0 C B:TRP285 5.0 27.7 1.0

Chlorine binding site 3 out of 3 in the Crystal Structure of IRAK4 Kinase Domain with Compound 9


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of IRAK4 Kinase Domain with Compound 9 within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl502 b:83.9 occ:1.00 OD2 C:ASP388 3.1 47.9 1.0 O C:HIS390 3.4 60.5 1.0 O D:HOH680 3.7 61.4 1.0 C C:HIS390 3.8 50.5 1.0 CG C:ASP388 3.8 44.3 1.0 CB C:ARG391 4.0 38.5 1.0 OD1 C:ASP388 4.0 37.1 1.0 N C:ARG391 4.2 47.4 1.0 CA C:ARG391 4.2 42.3 1.0 CG D:ARG391 4.2 40.7 1.0 CB C:HIS390 4.3 51.6 1.0 O C:HOH643 4.4 36.5 1.0 CB D:ARG391 4.5 41.3 1.0 CA C:HIS390 4.5 55.6 1.0 CD D:ARG391 4.7 40.5 1.0 CG C:ARG391 4.8 38.3 1.0 CA D:ARG391 4.8 39.6 1.0 O D:HOH662 4.9 42.5 1.0

M.M.Weiss, X.Zheng, N.Ji, C.M.Browne, V.Campbell, D.Chen, B.Enerson, X.Fei, X.Huang, C.R.Klaus, H.Li, M.Mayo, A.A.Mcdonald, A.Paul, H.Rong, K.Sharma, Y.Shi, A.Slavin, D.M.Walther, K.Yuan, Y.Zhang, X.Zhu, J.Kelleher, D.Walker, N.Mainolfi. Discovery of Kt-413, A Targeted Protein Degrader of IRAK4 and Imid Substrates Targeting MYD88 Mutant Diffuse Large B-Cell Lymphoma J.Med.Chem. 2024.
ISSN: ISSN 0022-2623
DOI: 10.1021/ACS.JMEDCHEM.3C01823