Bromine in PDB 7m0l: HPK1 in Complex with Compound 1

All present enzymatic activity of HPK1 in Complex with Compound 1:
2.7.11.1;

The structure of HPK1 in Complex with Compound 1, PDB code: 7m0l was solved by C.A.Lesburg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	87.59 / 2.43
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	44.85, 76.723, 88.413, 89.97, 97.84, 90.03
R / Rfree (%)	24.6 / 29.3

The binding sites of Bromine atom in the HPK1 in Complex with Compound 1 (pdb code 7m0l). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 4 binding sites of Bromine where determined in the HPK1 in Complex with Compound 1, PDB code: 7m0l:
Jump to Bromine binding site number: 1; 2; 3; 4;

Bromine binding site 1 out of 4 in the HPK1 in Complex with Compound 1


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of HPK1 in Complex with Compound 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Br301 b:70.2 occ:1.00 BR17 A:YK4301 0.0 70.2 1.0 C12 A:YK4301 1.9 36.1 1.0 C13 A:YK4301 2.8 45.8 1.0 C11 A:YK4301 2.9 44.6 1.0 N10 A:YK4301 3.1 44.0 1.0 O8 A:YK4301 3.6 52.7 1.0 CZ A:PHE156 3.7 154.7 1.0 CE1 A:PHE156 3.8 163.5 1.0 C14 A:YK4301 4.1 46.7 1.0 CB A:ALA154 4.2 94.0 1.0 C16 A:YK4301 4.2 51.1 1.0 CG2 A:VAL31 4.2 64.7 1.0 C4 A:YK4301 4.4 35.5 1.0 O A:HOH419 4.4 59.1 1.0 C15 A:YK4301 4.7 52.4 1.0 C7 A:YK4301 4.7 43.6 1.0 CE2 A:PHE156 4.8 152.2 1.0 CD1 A:PHE156 4.9 170.9 1.0 CD A:LYS46 5.0 78.0 1.0 NZ A:LYS46 5.0 78.9 0.0

Bromine binding site 2 out of 4 in the HPK1 in Complex with Compound 1


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of HPK1 in Complex with Compound 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Br301 b:101.1 occ:1.00 BR17 B:YK4301 0.0 101.1 1.0 C12 B:YK4301 1.9 102.0 1.0 C13 B:YK4301 2.8 103.0 1.0 C11 B:YK4301 2.9 93.3 1.0 N10 B:YK4301 3.1 87.4 1.0 O8 B:YK4301 3.5 82.5 1.0 CZ B:PHE156 3.8 134.9 1.0 CE1 B:PHE156 3.9 136.9 1.0 C14 B:YK4301 4.1 91.8 1.0 C16 B:YK4301 4.2 102.7 1.0 C4 B:YK4301 4.2 82.1 1.0 CB B:ALA154 4.4 110.9 1.0 C7 B:YK4301 4.5 81.9 1.0 CG2 B:VAL31 4.6 98.5 1.0 CE1 B:TYR28 4.6 112.0 1.0 C15 B:YK4301 4.7 89.9 1.0 CE2 B:PHE156 4.8 142.2 1.0 C5 B:YK4301 4.8 68.5 1.0 CD1 B:PHE156 4.9 144.5 1.0 O B:HOH405 4.9 66.3 1.0 CD1 B:TYR28 5.0 112.8 1.0

Bromine binding site 3 out of 4 in the HPK1 in Complex with Compound 1


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of HPK1 in Complex with Compound 1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Br301 b:96.4 occ:1.00 BR17 C:YK4301 0.0 96.4 1.0 C12 C:YK4301 1.9 96.7 1.0 C13 C:YK4301 2.8 105.5 1.0 C11 C:YK4301 2.9 102.1 1.0 N10 C:YK4301 3.1 103.5 1.0 O8 C:YK4301 3.6 93.2 1.0 CE1 C:PHE156 3.6 136.7 1.0 CZ C:PHE156 3.7 136.5 1.0 C14 C:YK4301 4.1 109.2 1.0 C16 C:YK4301 4.2 100.3 1.0 C4 C:YK4301 4.2 97.8 1.0 CB C:ALA154 4.4 108.8 1.0 C7 C:YK4301 4.6 87.4 1.0 CD1 C:PHE156 4.6 142.2 1.0 CG2 C:VAL31 4.6 97.2 1.0 CE1 C:TYR28 4.7 118.7 1.0 C15 C:YK4301 4.7 94.6 1.0 CE2 C:PHE156 4.8 140.8 1.0 C5 C:YK4301 4.8 77.2 1.0 CD1 C:TYR28 5.0 117.7 1.0

Bromine binding site 4 out of 4 in the HPK1 in Complex with Compound 1


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of HPK1 in Complex with Compound 1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Br301 b:70.0 occ:1.00 BR17 D:YK4301 0.0 70.0 1.0 C12 D:YK4301 1.9 35.1 1.0 C13 D:YK4301 2.8 44.1 1.0 C11 D:YK4301 2.9 45.7 1.0 N10 D:YK4301 3.1 43.9 1.0 O D:HOH419 3.5 75.1 1.0 O8 D:YK4301 3.6 48.1 1.0 CZ D:PHE156 3.9 149.4 1.0 CE1 D:PHE156 4.0 151.3 1.0 CB D:ALA154 4.1 86.5 1.0 C14 D:YK4301 4.1 37.6 1.0 C16 D:YK4301 4.2 49.8 1.0 CG2 D:VAL31 4.3 65.8 1.0 C4 D:YK4301 4.4 35.1 1.0 C15 D:YK4301 4.7 44.9 1.0 C7 D:YK4301 4.7 38.8 1.0 NZ D:LYS46 4.8 77.7 0.0 CE2 D:PHE156 4.8 150.6 1.0

B.A.Vara, S.M.Levi, A.Achab, D.A.Candito, X.Fradera, C.Lesburg, S.Kawamura, B.M.Lacey, J.Lim, J.L.Methot, Z.Xu, H.Xu, D.M.Smith, J.Piesvaux, J.R.Miller, M.Bittinger, J.Bennett, E.F.Dimauro, A.Pasternak. Discovery of Diaminopyrimidine Carboxamide HPK1 Inhibitors As Preclinical Immunotherapy Tool Compounds Acs Med.Chem.Lett. 2021.
ISSN: ISSN 1948-5875
DOI: 10.1021/ACSMEDCHEMLETT.1C00096