Fluorine in PDB 9nc2: Structure of HPK1 with Compound C3

All present enzymatic activity of Structure of HPK1 with Compound C3:
2.7.11.1;

The structure of Structure of HPK1 with Compound C3, PDB code: 9nc2 was solved by J.R.Kiefer, B.T.Walters, W.Wang, P.Wu, Y.Duo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.50 / 1.50
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	52.006, 57.963, 61.562, 70.36, 66.43, 68.57
R / Rfree (%)	15.8 / 18.2

The structure of Structure of HPK1 with Compound C3 also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Fluorine atom in the Structure of HPK1 with Compound C3 (pdb code 9nc2). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Structure of HPK1 with Compound C3, PDB code: 9nc2:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Structure of HPK1 with Compound C3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of HPK1 with Compound C3 within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:26.5 occ:1.00 F25 A:F97301 0.0 26.5 1.0 C23 A:F97301 1.3 21.1 1.0 F26 A:F97301 2.3 18.8 1.0 C24 A:F97301 2.4 12.3 1.0 C22 A:F97301 2.4 18.6 1.0 H7 A:F97301 2.4 14.8 1.0 H5 A:F97301 2.6 22.4 1.0 HH A:TYR28 2.7 58.1 1.0 H6 A:F97301 2.9 22.4 1.0 H8 A:F97301 2.9 14.8 1.0 HG21 A:VAL31 3.0 19.9 1.0 OH A:TYR28 3.0 48.4 1.0 HG23 A:VAL31 3.2 19.9 1.0 N20 A:F97301 3.4 11.4 1.0 C21 A:F97301 3.5 15.6 1.0 CG2 A:VAL31 3.5 16.6 1.0 HE1 A:TYR28 3.6 47.5 1.0 CZ A:TYR28 3.6 47.6 1.0 HB A:VAL31 3.6 14.6 1.0 O1 A:EDO302 3.7 28.5 1.0 CE1 A:TYR28 3.8 39.6 1.0 H4 A:F97301 4.0 18.8 1.0 HO1 A:EDO302 4.0 34.2 1.0 H14 A:F97301 4.0 17.5 1.0 CB A:VAL31 4.1 12.1 1.0 HA3 A:GLY24 4.3 22.2 1.0 H3 A:F97301 4.3 18.8 1.0 HG22 A:VAL31 4.4 19.9 1.0 HG11 A:VAL31 4.5 19.7 1.0 H21 A:EDO302 4.5 27.6 1.0 CE2 A:TYR28 4.5 54.3 1.0 H12 A:F97301 4.6 17.2 1.0 O2 A:EDO302 4.6 23.5 1.0 C1 A:EDO302 4.7 24.0 1.0 C18 A:F97301 4.7 12.0 1.0 HE2 A:TYR28 4.8 65.2 1.0 C2 A:EDO302 4.8 23.0 1.0 HO2 A:EDO302 4.8 28.2 1.0 H11 A:EDO302 4.8 28.9 1.0 H17 A:F97301 4.9 18.5 1.0 CD1 A:TYR28 4.9 45.0 1.0 CG1 A:VAL31 4.9 16.4 1.0 H1 A:F97301 4.9 14.1 1.0 C2 A:F97301 4.9 14.6 1.0 CA A:GLY24 4.9 18.5 1.0 C A:GLY24 5.0 20.6 1.0

Fluorine binding site 2 out of 4 in the Structure of HPK1 with Compound C3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of HPK1 with Compound C3 within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:18.8 occ:1.00 F26 A:F97301 0.0 18.8 1.0 C23 A:F97301 1.4 21.1 1.0 F25 A:F97301 2.3 26.5 1.0 C22 A:F97301 2.4 18.6 1.0 C24 A:F97301 2.4 12.3 1.0 H8 A:F97301 2.5 14.8 1.0 HB A:VAL31 2.5 14.6 1.0 H4 A:F97301 2.6 18.8 1.0 H6 A:F97301 2.6 22.4 1.0 HA3 A:GLY24 2.7 22.2 1.0 C21 A:F97301 2.8 15.6 1.0 N20 A:F97301 3.0 11.4 1.0 HB2 A:LEU23 3.0 15.1 1.0 N A:GLY24 3.1 17.0 1.0 HH A:TYR28 3.1 58.1 1.0 CA A:GLY24 3.2 18.5 1.0 H7 A:F97301 3.3 14.8 1.0 H A:GLY24 3.3 20.4 1.0 H5 A:F97301 3.3 22.4 1.0 C A:LEU23 3.3 17.1 1.0 HG23 A:VAL31 3.4 19.9 1.0 CB A:VAL31 3.4 12.1 1.0 C A:GLY24 3.5 20.6 1.0 HG21 A:VAL31 3.6 19.9 1.0 HB3 A:LEU23 3.6 15.1 1.0 O A:LEU23 3.6 18.9 1.0 CG2 A:VAL31 3.6 16.6 1.0 CB A:LEU23 3.7 12.6 1.0 O A:GLY24 3.8 17.2 1.0 OH A:TYR28 3.8 48.4 1.0 H3 A:F97301 3.8 18.8 1.0 H A:VAL31 3.9 17.1 1.0 HA2 A:GLY24 4.1 22.2 1.0 CA A:LEU23 4.1 14.8 1.0 C18 A:F97301 4.2 12.0 1.0 HE1 A:TYR28 4.2 47.5 1.0 HG11 A:VAL31 4.2 19.7 1.0 N A:GLY25 4.3 26.1 1.0 O A:VAL31 4.3 14.7 1.0 CG1 A:VAL31 4.3 16.4 1.0 CA A:VAL31 4.4 13.7 1.0 N A:VAL31 4.4 14.2 1.0 HG12 A:VAL31 4.5 19.7 1.0 H A:GLY25 4.5 31.4 1.0 HG22 A:VAL31 4.6 19.9 1.0 H A:LEU23 4.6 17.8 1.0 HD12 A:LEU23 4.7 25.9 1.0 CZ A:TYR28 4.7 47.6 1.0 C A:VAL31 4.7 15.0 1.0 O A:HOH518 4.8 32.1 1.0 CE1 A:TYR28 4.8 39.6 1.0 N19 A:F97301 4.8 9.4 1.0 N A:LEU23 4.8 14.8 1.0 HA A:LEU23 4.9 17.8 1.0 HA2 A:GLY25 5.0 39.7 1.0

Fluorine binding site 3 out of 4 in the Structure of HPK1 with Compound C3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of HPK1 with Compound C3 within 5.0Å range: probe atom residue distance (Å) B Occ B:F301 b:30.8 occ:1.00 F25 B:F97301 0.0 30.8 1.0 C23 B:F97301 1.3 24.3 1.0 F26 B:F97301 2.2 24.0 1.0 C24 B:F97301 2.4 17.0 1.0 C22 B:F97301 2.4 20.4 1.0 H6 B:F97301 2.5 24.5 1.0 H8 B:F97301 2.5 20.4 1.0 H7 B:F97301 2.9 20.4 1.0 O B:HOH708 2.9 33.6 1.0 H5 B:F97301 3.0 24.5 1.0 HG21 B:VAL31 3.1 25.4 1.0 HH B:TYR28 3.1 57.9 1.0 OH B:TYR28 3.4 48.2 1.0 N20 B:F97301 3.4 16.3 1.0 C21 B:F97301 3.5 24.9 1.0 H14 B:F97301 3.6 17.9 1.0 O B:HOH513 3.7 43.3 1.0 CG2 B:VAL31 3.8 21.2 1.0 HB B:VAL31 3.8 28.0 1.0 HG23 B:VAL31 3.8 25.4 1.0 H12 B:F97301 3.9 24.3 1.0 O B:HOH693 4.1 25.1 1.0 HG11 B:VAL31 4.1 23.5 1.0 H3 B:F97301 4.1 29.9 1.0 H4 B:F97301 4.2 29.9 1.0 CB B:VAL31 4.3 23.3 1.0 HA3 B:GLY24 4.4 29.2 1.0 H16 B:F97301 4.5 20.8 1.0 C2 B:F97301 4.5 14.9 1.0 C1 B:F97301 4.6 20.2 1.0 HG22 B:VAL31 4.7 25.4 1.0 CZ B:TYR28 4.7 57.1 1.0 H13 B:F97301 4.7 24.3 1.0 C18 B:F97301 4.7 15.9 1.0 CG1 B:VAL31 4.7 19.5 1.0 H1 B:F97301 4.8 15.1 1.0 O B:HOH479 5.0 22.1 1.0 H B:GLY25 5.0 40.8 1.0

Fluorine binding site 4 out of 4 in the Structure of HPK1 with Compound C3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of HPK1 with Compound C3 within 5.0Å range: probe atom residue distance (Å) B Occ B:F301 b:24.0 occ:1.00 F26 B:F97301 0.0 24.0 1.0 C23 B:F97301 1.4 24.3 1.0 F25 B:F97301 2.2 30.8 1.0 C24 B:F97301 2.4 17.0 1.0 C22 B:F97301 2.4 20.4 1.0 H7 B:F97301 2.5 20.4 1.0 H5 B:F97301 2.5 24.5 1.0 HB B:VAL31 2.6 28.0 1.0 HA3 B:GLY24 2.7 29.2 1.0 N20 B:F97301 2.8 16.3 1.0 C21 B:F97301 3.0 24.9 1.0 HB2 B:LEU23 3.1 23.8 1.0 H4 B:F97301 3.2 29.9 1.0 N B:GLY24 3.3 25.2 1.0 H8 B:F97301 3.3 20.4 1.0 H6 B:F97301 3.3 24.5 1.0 CA B:GLY24 3.3 24.3 1.0 C B:LEU23 3.4 24.9 1.0 HG21 B:VAL31 3.5 25.4 1.0 CB B:VAL31 3.5 23.3 1.0 HB3 B:LEU23 3.5 23.8 1.0 H B:GLY24 3.6 30.3 1.0 O B:LEU23 3.7 25.7 1.0 C B:GLY24 3.7 35.2 1.0 HG23 B:VAL31 3.7 25.4 1.0 CB B:LEU23 3.7 19.8 1.0 CG2 B:VAL31 3.8 21.2 1.0 HG11 B:VAL31 3.8 23.5 1.0 H3 B:F97301 4.0 29.9 1.0 CG1 B:VAL31 4.1 19.5 1.0 N B:GLY25 4.1 34.0 1.0 O B:GLY24 4.1 28.3 1.0 C18 B:F97301 4.2 15.9 1.0 O B:HOH513 4.2 43.3 1.0 HG12 B:VAL31 4.2 23.5 1.0 HA2 B:GLY24 4.2 29.2 1.0 CA B:LEU23 4.2 19.2 1.0 H B:GLY25 4.2 40.8 1.0 HH B:TYR28 4.3 57.9 1.0 OH B:TYR28 4.3 48.2 1.0 H B:VAL31 4.4 26.2 1.0 CA B:VAL31 4.7 17.4 1.0 O B:VAL31 4.7 20.7 1.0 HG22 B:VAL31 4.7 25.4 1.0 HD12 B:LEU23 4.7 27.4 1.0 N19 B:F97301 4.7 12.8 1.0 HA2 B:GLY25 4.8 59.0 1.0 H B:LEU23 4.9 27.2 1.0 N B:VAL31 4.9 21.8 1.0 H14 B:F97301 4.9 17.9 1.0 HA B:LEU23 4.9 23.1 1.0 HG13 B:VAL31 5.0 23.5 1.0 HD13 B:LEU23 5.0 27.4 1.0

B.T.Walters, A.W.Patapoff, J.R.Kiefer, P.Wu, W.Wang. Integrating Hydrogen Exchange with Molecular Dynamics For Improved Ligand Binding Predictions. J.Chem.Inf.Model. 2025.
ISSN: ESSN 1549-960X
PubMed: 40495786
DOI: 10.1021/ACS.JCIM.5C00397