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Fluorine in PDB 7m0m: HPK1 in Complex with Compound 1

Enzymatic activity of HPK1 in Complex with Compound 1

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

Protein crystallography data

The structure of HPK1 in Complex with Compound 1, PDB code: 7m0m 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) 63.31 / 1.93
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 51.168, 56.994, 63.459, 86.73, 86.63, 67.06
R / Rfree (%) 18.6 / 22

Fluorine Binding Sites:

The binding sites of Fluorine atom in the HPK1 in Complex with Compound 1 (pdb code 7m0m). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the HPK1 in Complex with Compound 1, PDB code: 7m0m:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 7m0m

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Fluorine binding site 1 out of 8 in the HPK1 in Complex with Compound 1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of HPK1 in Complex with Compound 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:31.1
occ:1.00
 F17 A:YK1301 0.0 31.1 1.0
C16 A:YK1301 1.3 32.2 1.0
C15 A:YK1301 2.3 35.6 1.0
C11 A:YK1301 2.4 33.9 1.0
N3 A:YK1301 2.7 24.2 1.0
N10 A:YK1301 2.8 31.9 1.0
C4 A:YK1301 3.0 28.3 1.0
CB A:VAL31 3.0 33.9 1.0
CG1 A:VAL31 3.1 32.4 1.0
CB A:LEU23 3.3 37.7 1.0
CD1 A:LEU23 3.5 38.1 1.0
CG2 A:VAL31 3.5 36.1 1.0
C14 A:YK1301 3.6 33.8 1.0
C12 A:YK1301 3.6 32.8 1.0
C24 A:YK1301 3.7 29.7 1.0
C2 A:YK1301 3.7 24.3 1.0
CG A:LEU23 4.0 36.1 1.0
C13 A:YK1301 4.1 32.7 1.0
C5 A:YK1301 4.1 27.6 1.0
C23 A:YK1301 4.2 27.4 1.0
N22 A:YK1301 4.3 26.0 1.0
CA A:VAL31 4.4 35.3 1.0
C25 A:YK1301 4.5 26.6 1.0
CA A:LEU23 4.5 42.3 1.0
C A:LEU23 4.6 44.7 1.0
N1 A:YK1301 4.6 22.7 1.0
O A:VAL31 4.6 34.8 1.0
C34 A:YK1301 4.7 28.2 1.0
C A:VAL31 4.7 34.4 1.0
O A:GLY24 4.7 46.5 1.0
O A:LEU23 4.8 55.2 1.0
C6 A:YK1301 4.8 24.8 1.0
N A:GLY24 4.9 45.1 1.0
C18 A:YK1301 4.9 36.8 1.0

Fluorine binding site 2 out of 8 in 7m0m

Go back to Fluorine Binding Sites List in 7m0m
Fluorine binding site 2 out of 8 in the HPK1 in Complex with Compound 1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of HPK1 in Complex with Compound 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:37.7
occ:1.00
 F19 A:YK1301 0.0 37.7 1.0
C18 A:YK1301 1.4 36.8 1.0
F21 A:YK1301 2.2 34.5 1.0
F20 A:YK1301 2.3 41.2 1.0
C12 A:YK1301 2.4 32.8 1.0
N10 A:YK1301 2.9 31.9 1.0
C11 A:YK1301 3.0 33.9 1.0
O A:HOH549 3.2 41.1 1.0
O A:HOH449 3.2 44.6 1.0
CB A:ASP155 3.4 39.6 1.0
O8 A:YK1301 3.4 30.2 1.0
C13 A:YK1301 3.5 32.7 1.0
N A:ASP155 3.5 32.8 1.0
CA A:ASP155 3.8 37.6 1.0
CB A:ALA154 4.0 31.8 1.0
CG A:ASP155 4.1 44.8 1.0
C4 A:YK1301 4.1 28.3 1.0
OD2 A:ASP155 4.2 59.7 1.0
C16 A:YK1301 4.3 32.2 1.0
C A:ALA154 4.4 32.3 1.0
C7 A:YK1301 4.5 30.1 1.0
C14 A:YK1301 4.7 33.8 1.0
C5 A:YK1301 4.7 27.6 1.0
CA A:ALA154 4.8 30.4 1.0
O A:HOH484 4.9 44.6 1.0
OD1 A:ASP155 4.9 47.2 1.0
CD1 A:LEU144 4.9 31.5 1.0

Fluorine binding site 3 out of 8 in 7m0m

Go back to Fluorine Binding Sites List in 7m0m
Fluorine binding site 3 out of 8 in the HPK1 in Complex with Compound 1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of HPK1 in Complex with Compound 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:41.2
occ:1.00
 F20 A:YK1301 0.0 41.2 1.0
C18 A:YK1301 1.4 36.8 1.0
F21 A:YK1301 2.2 34.5 1.0
F19 A:YK1301 2.3 37.7 1.0
C12 A:YK1301 2.4 32.8 1.0
C13 A:YK1301 2.8 32.7 1.0
OD1 A:ASN142 3.2 36.0 1.0
CB A:ASP155 3.3 39.6 1.0
OD2 A:ASP155 3.5 59.7 1.0
C11 A:YK1301 3.7 33.9 1.0
CG A:ASP155 3.9 44.8 1.0
O A:ALA141 3.9 28.8 1.0
C14 A:YK1301 4.1 33.8 1.0
O A:HOH434 4.2 35.0 1.0
O A:HOH572 4.2 45.2 1.0
N10 A:YK1301 4.3 31.9 1.0
CA A:GLY26 4.3 43.5 1.0
CG A:ASN142 4.4 32.4 1.0
CA A:ASP155 4.4 37.6 1.0
N A:ASP155 4.5 32.8 1.0
O A:HOH549 4.5 41.1 1.0
CA A:ASN142 4.6 27.6 1.0
C A:ALA141 4.8 29.9 1.0
CB A:ALA154 4.8 31.8 1.0
C16 A:YK1301 4.8 32.2 1.0
C A:ALA154 4.9 32.3 1.0
CB A:ASN142 5.0 30.3 1.0

Fluorine binding site 4 out of 8 in 7m0m

Go back to Fluorine Binding Sites List in 7m0m
Fluorine binding site 4 out of 8 in the HPK1 in Complex with Compound 1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of HPK1 in Complex with Compound 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:34.5
occ:1.00
 F21 A:YK1301 0.0 34.5 1.0
C18 A:YK1301 1.4 36.8 1.0
F20 A:YK1301 2.2 41.2 1.0
F19 A:YK1301 2.2 37.7 1.0
C12 A:YK1301 2.3 32.8 1.0
C11 A:YK1301 2.9 33.9 1.0
N10 A:YK1301 2.9 31.9 1.0
CD2 A:LEU144 3.4 33.2 1.0
C13 A:YK1301 3.4 32.7 1.0
CD1 A:LEU144 3.4 31.5 1.0
CB A:ALA154 3.5 31.8 1.0
C4 A:YK1301 3.6 28.3 1.0
CG A:LEU144 3.7 31.1 1.0
N3 A:YK1301 4.1 24.2 1.0
O8 A:YK1301 4.1 30.2 1.0
C16 A:YK1301 4.2 32.2 1.0
O A:ALA141 4.2 28.8 1.0
C5 A:YK1301 4.4 27.6 1.0
N A:ASP155 4.5 32.8 1.0
C14 A:YK1301 4.6 33.8 1.0
CB A:ASP155 4.6 39.6 1.0
O A:HOH449 4.6 44.6 1.0
O A:HOH434 4.6 35.0 1.0
C7 A:YK1301 4.7 30.1 1.0
CA A:ALA154 4.8 30.4 1.0
C A:ALA154 4.8 32.3 1.0
OD1 A:ASN142 4.8 36.0 1.0
C15 A:YK1301 4.9 35.6 1.0
CA A:ASN142 4.9 27.6 1.0

Fluorine binding site 5 out of 8 in 7m0m

Go back to Fluorine Binding Sites List in 7m0m
Fluorine binding site 5 out of 8 in the HPK1 in Complex with Compound 1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of HPK1 in Complex with Compound 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F301

b:31.7
occ:1.00
 F17 B:YK1301 0.0 31.7 1.0
C16 B:YK1301 1.3 32.9 1.0
C15 B:YK1301 2.3 35.3 1.0
C11 B:YK1301 2.4 31.2 1.0
N10 B:YK1301 2.8 31.5 1.0
N3 B:YK1301 2.8 22.4 1.0
C4 B:YK1301 3.0 26.3 1.0
CB B:VAL31 3.1 31.5 1.0
CG1 B:VAL31 3.1 32.7 1.0
CB B:LEU23 3.3 38.4 1.0
CD1 B:LEU23 3.4 34.5 1.0
C14 B:YK1301 3.6 35.9 1.0
CG2 B:VAL31 3.6 32.4 1.0
C12 B:YK1301 3.6 34.5 1.0
C24 B:YK1301 3.7 35.0 1.0
C2 B:YK1301 3.8 25.9 1.0
CG B:LEU23 4.0 39.2 1.0
C13 B:YK1301 4.1 33.3 1.0
C23 B:YK1301 4.2 33.7 1.0
C5 B:YK1301 4.2 26.9 1.0
N22 B:YK1301 4.3 29.8 1.0
CA B:VAL31 4.4 33.5 1.0
C25 B:YK1301 4.4 36.6 1.0
CA B:LEU23 4.6 40.1 1.0
C B:LEU23 4.6 39.8 1.0
O B:VAL31 4.6 33.6 1.0
C B:VAL31 4.6 33.0 1.0
C34 B:YK1301 4.7 34.1 1.0
N1 B:YK1301 4.7 26.2 1.0
O B:GLY24 4.8 47.9 1.0
O B:LEU23 4.8 45.8 1.0
C6 B:YK1301 4.9 22.6 1.0
C18 B:YK1301 4.9 30.7 1.0
N B:GLY24 4.9 42.0 1.0

Fluorine binding site 6 out of 8 in 7m0m

Go back to Fluorine Binding Sites List in 7m0m
Fluorine binding site 6 out of 8 in the HPK1 in Complex with Compound 1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of HPK1 in Complex with Compound 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F301

b:36.4
occ:1.00
 F19 B:YK1301 0.0 36.4 1.0
C18 B:YK1301 1.4 30.7 1.0
F21 B:YK1301 2.2 35.2 1.0
F20 B:YK1301 2.3 36.5 1.0
C12 B:YK1301 2.4 34.5 1.0
N10 B:YK1301 2.9 31.5 1.0
C11 B:YK1301 3.0 31.2 1.0
O B:HOH456 3.2 36.1 1.0
O8 B:YK1301 3.3 29.4 1.0
O B:HOH447 3.5 46.5 1.0
C13 B:YK1301 3.5 33.3 1.0
CB B:ASP155 3.5 33.4 1.0
N B:ASP155 3.8 28.9 1.0
CA B:ASP155 3.9 34.0 1.0
CB B:ALA154 4.0 33.8 1.0
C4 B:YK1301 4.0 26.3 1.0
CG B:ASP155 4.1 36.7 1.0
OD2 B:ASP155 4.2 37.4 1.0
C16 B:YK1301 4.3 32.9 1.0
C7 B:YK1301 4.3 26.5 1.0
C B:ALA154 4.5 31.6 1.0
C5 B:YK1301 4.6 26.9 1.0
O B:HOH462 4.6 52.7 1.0
C14 B:YK1301 4.7 35.9 1.0
CA B:ALA154 4.9 33.0 1.0
CA B:GLY26 4.9 43.5 1.0
N3 B:YK1301 5.0 22.4 1.0
OD1 B:ASP155 5.0 37.7 1.0

Fluorine binding site 7 out of 8 in 7m0m

Go back to Fluorine Binding Sites List in 7m0m
Fluorine binding site 7 out of 8 in the HPK1 in Complex with Compound 1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of HPK1 in Complex with Compound 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F301

b:36.5
occ:1.00
 F20 B:YK1301 0.0 36.5 1.0
C18 B:YK1301 1.4 30.7 1.0
F21 B:YK1301 2.3 35.2 1.0
F19 B:YK1301 2.3 36.4 1.0
C12 B:YK1301 2.4 34.5 1.0
C13 B:YK1301 2.8 33.3 1.0
O B:HOH407 3.1 41.0 1.0
OD1 B:ASN142 3.2 35.0 1.0
CB B:ASP155 3.4 33.4 1.0
OD2 B:ASP155 3.4 37.4 1.0
C11 B:YK1301 3.7 31.2 1.0
CG B:ASP155 3.8 36.7 1.0
O B:HOH544 3.9 40.6 1.0
CA B:GLY26 4.1 43.5 1.0
O B:ALA141 4.1 32.8 1.0
C14 B:YK1301 4.1 35.9 1.0
O B:HOH414 4.3 36.3 1.0
N10 B:YK1301 4.3 31.5 1.0
CG B:ASN142 4.4 33.6 1.0
CA B:ASP155 4.5 34.0 1.0
O B:HOH456 4.6 36.1 1.0
N B:ASP155 4.6 28.9 1.0
N B:GLY26 4.8 45.9 1.0
CA B:ASN142 4.8 31.4 1.0
C16 B:YK1301 4.8 32.9 1.0
CB B:ALA154 4.9 33.8 1.0
OD1 B:ASP155 5.0 37.7 1.0
C B:ALA141 5.0 34.1 1.0
C B:ALA154 5.0 31.6 1.0

Fluorine binding site 8 out of 8 in 7m0m

Go back to Fluorine Binding Sites List in 7m0m
Fluorine binding site 8 out of 8 in the HPK1 in Complex with Compound 1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of HPK1 in Complex with Compound 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F301

b:35.2
occ:1.00
 F21 B:YK1301 0.0 35.2 1.0
C18 B:YK1301 1.4 30.7 1.0
F19 B:YK1301 2.2 36.4 1.0
F20 B:YK1301 2.3 36.5 1.0
C12 B:YK1301 2.3 34.5 1.0
C11 B:YK1301 2.9 31.2 1.0
N10 B:YK1301 3.0 31.5 1.0
C13 B:YK1301 3.4 33.3 1.0
CD2 B:LEU144 3.5 34.0 1.0
CD1 B:LEU144 3.5 33.1 1.0
CB B:ALA154 3.5 33.8 1.0
C4 B:YK1301 3.6 26.3 1.0
CG B:LEU144 3.8 31.3 1.0
O8 B:YK1301 4.1 29.4 1.0
N3 B:YK1301 4.1 22.4 1.0
O B:ALA141 4.2 32.8 1.0
C16 B:YK1301 4.3 32.9 1.0
C5 B:YK1301 4.4 26.9 1.0
O B:HOH414 4.6 36.3 1.0
C14 B:YK1301 4.6 35.9 1.0
CB B:ASP155 4.6 33.4 1.0
OD1 B:ASN142 4.6 35.0 1.0
N B:ASP155 4.6 28.9 1.0
C7 B:YK1301 4.6 26.5 1.0
CA B:ALA154 4.7 33.0 1.0
C B:ALA154 4.8 31.6 1.0
CA B:ASN142 4.9 31.4 1.0
C15 B:YK1301 4.9 35.3 1.0

Reference:

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
Page generated: Tue Jul 15 21:27:25 2025

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