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Chlorine in PDB 8fko: Crystal Structure of HPK1 Kinase Domain T165E,S171E Phosphomimetic Mutant in Complex with 3-{4-[(2S,5R)-5-Amino-2-Methylpiperidin-1-Yl]- 6-Chloro-7H-Pyrrolo[2,3-D]Pyrimidin-5-Yl}Benzonitrile

Enzymatic activity of Crystal Structure of HPK1 Kinase Domain T165E,S171E Phosphomimetic Mutant in Complex with 3-{4-[(2S,5R)-5-Amino-2-Methylpiperidin-1-Yl]- 6-Chloro-7H-Pyrrolo[2,3-D]Pyrimidin-5-Yl}Benzonitrile

All present enzymatic activity of Crystal Structure of HPK1 Kinase Domain T165E,S171E Phosphomimetic Mutant in Complex with 3-{4-[(2S,5R)-5-Amino-2-Methylpiperidin-1-Yl]- 6-Chloro-7H-Pyrrolo[2,3-D]Pyrimidin-5-Yl}Benzonitrile:
2.7.11.1;

Protein crystallography data

The structure of Crystal Structure of HPK1 Kinase Domain T165E,S171E Phosphomimetic Mutant in Complex with 3-{4-[(2S,5R)-5-Amino-2-Methylpiperidin-1-Yl]- 6-Chloro-7H-Pyrrolo[2,3-D]Pyrimidin-5-Yl}Benzonitrile, PDB code: 8fko was solved by M.Mctigue, E.Johnson, C.Cronin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 52.91 / 2.10
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 58.074, 86.996, 109.817, 95.73, 100.64, 108.89
R / Rfree (%) 22 / 25.8

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of HPK1 Kinase Domain T165E,S171E Phosphomimetic Mutant in Complex with 3-{4-[(2S,5R)-5-Amino-2-Methylpiperidin-1-Yl]- 6-Chloro-7H-Pyrrolo[2,3-D]Pyrimidin-5-Yl}Benzonitrile (pdb code 8fko). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Crystal Structure of HPK1 Kinase Domain T165E,S171E Phosphomimetic Mutant in Complex with 3-{4-[(2S,5R)-5-Amino-2-Methylpiperidin-1-Yl]- 6-Chloro-7H-Pyrrolo[2,3-D]Pyrimidin-5-Yl}Benzonitrile, PDB code: 8fko:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 8fko

Go back to Chlorine Binding Sites List in 8fko
Chlorine binding site 1 out of 5 in the Crystal Structure of HPK1 Kinase Domain T165E,S171E Phosphomimetic Mutant in Complex with 3-{4-[(2S,5R)-5-Amino-2-Methylpiperidin-1-Yl]- 6-Chloro-7H-Pyrrolo[2,3-D]Pyrimidin-5-Yl}Benzonitrile


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 HPK1 Kinase Domain T165E,S171E Phosphomimetic Mutant in Complex with 3-{4-[(2S,5R)-5-Amino-2-Methylpiperidin-1-Yl]- 6-Chloro-7H-Pyrrolo[2,3-D]Pyrimidin-5-Yl}Benzonitrile within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl401

b:42.5
occ:1.00
 CL1 A:Y3O401 0.0 42.5 1.0
C10 A:Y3O401 1.7 36.1 1.0
N2 A:Y3O401 2.6 33.8 1.0
C9 A:Y3O401 2.8 33.4 1.0
CE A:MET91 3.1 50.0 1.0
C7 A:Y3O401 3.4 33.4 1.0
C8 A:Y3O401 3.4 33.0 1.0
SD A:MET91 3.6 54.9 1.0
O A:HOH610 3.7 28.1 1.0
CG2 A:VAL75 3.7 28.0 1.0
C12 A:Y3O401 3.8 32.4 1.0
CB A:MET91 3.9 35.7 1.0
O A:GLU92 3.9 28.4 1.0
C13 A:Y3O401 3.9 32.0 1.0
CD1 A:LEU144 4.1 27.5 1.0
CG A:MET91 4.4 42.2 1.0
CG1 A:VAL75 4.5 27.9 1.0
CB A:ALA44 4.5 33.2 1.0
CB A:ALA154 4.5 22.9 1.0
C6 A:Y3O401 4.5 34.1 1.0
C3 A:Y3O401 4.5 32.1 1.0
CB A:VAL75 4.6 27.3 1.0

Chlorine binding site 2 out of 5 in 8fko

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Chlorine binding site 2 out of 5 in the Crystal Structure of HPK1 Kinase Domain T165E,S171E Phosphomimetic Mutant in Complex with 3-{4-[(2S,5R)-5-Amino-2-Methylpiperidin-1-Yl]- 6-Chloro-7H-Pyrrolo[2,3-D]Pyrimidin-5-Yl}Benzonitrile


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 HPK1 Kinase Domain T165E,S171E Phosphomimetic Mutant in Complex with 3-{4-[(2S,5R)-5-Amino-2-Methylpiperidin-1-Yl]- 6-Chloro-7H-Pyrrolo[2,3-D]Pyrimidin-5-Yl}Benzonitrile within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl401

b:42.6
occ:1.00
 CL1 B:Y3O401 0.0 42.6 1.0
C10 B:Y3O401 1.7 36.7 1.0
N2 B:Y3O401 2.6 34.6 1.0
C9 B:Y3O401 2.8 34.6 1.0
C8 B:Y3O401 3.4 34.5 1.0
C7 B:Y3O401 3.4 35.0 1.0
CE B:MET91 3.5 52.4 1.0
SD B:MET91 3.5 55.8 1.0
CB B:MET91 3.6 37.6 1.0
CG2 B:VAL75 3.8 33.4 1.0
O B:HOH570 3.8 38.0 1.0
C12 B:Y3O401 3.8 33.2 1.0
C13 B:Y3O401 3.9 32.9 1.0
O B:GLU92 4.0 34.4 1.0
CG1 B:VAL75 4.1 32.0 1.0
CG B:MET91 4.2 42.5 1.0
CD1 B:LEU144 4.3 28.1 1.0
CB B:VAL75 4.4 31.9 1.0
CB B:ALA44 4.4 34.4 1.0
C3 B:Y3O401 4.5 34.4 1.0
C6 B:Y3O401 4.5 35.9 1.0
CB B:ALA154 4.5 25.5 1.0
CA B:MET91 5.0 35.6 1.0
N4 B:Y3O401 5.0 32.4 1.0

Chlorine binding site 3 out of 5 in 8fko

Go back to Chlorine Binding Sites List in 8fko
Chlorine binding site 3 out of 5 in the Crystal Structure of HPK1 Kinase Domain T165E,S171E Phosphomimetic Mutant in Complex with 3-{4-[(2S,5R)-5-Amino-2-Methylpiperidin-1-Yl]- 6-Chloro-7H-Pyrrolo[2,3-D]Pyrimidin-5-Yl}Benzonitrile


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 HPK1 Kinase Domain T165E,S171E Phosphomimetic Mutant in Complex with 3-{4-[(2S,5R)-5-Amino-2-Methylpiperidin-1-Yl]- 6-Chloro-7H-Pyrrolo[2,3-D]Pyrimidin-5-Yl}Benzonitrile within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl401

b:42.3
occ:1.00
 CL1 C:Y3O401 0.0 42.3 1.0
C10 C:Y3O401 1.7 37.3 1.0
N2 C:Y3O401 2.6 35.0 1.0
C9 C:Y3O401 2.8 35.2 1.0
CE C:MET91 3.3 52.1 1.0
C7 C:Y3O401 3.3 35.6 1.0
C8 C:Y3O401 3.4 35.2 1.0
O C:HOH574 3.4 32.6 1.0
O C:GLU92 3.7 31.7 1.0
CB C:MET91 3.7 34.6 1.0
C12 C:Y3O401 3.8 33.2 1.0
SD C:MET91 3.8 55.0 1.0
C13 C:Y3O401 3.9 33.0 1.0
CG1 C:VAL75 4.0 33.4 1.0
CB C:ALA44 4.0 35.0 1.0
CG2 C:VAL75 4.3 33.2 1.0
CB C:VAL75 4.3 32.9 1.0
CD1 C:LEU144 4.4 27.4 1.0
CG C:MET91 4.4 40.6 1.0
C6 C:Y3O401 4.5 36.5 1.0
CB C:ALA154 4.5 25.4 1.0
C3 C:Y3O401 4.6 35.4 1.0
C C:GLU92 4.8 31.8 1.0
C C:MET91 4.9 31.7 1.0
CA C:MET91 5.0 32.9 1.0
N C:GLU92 5.0 30.6 1.0
C1 C:Y3O401 5.0 38.4 1.0

Chlorine binding site 4 out of 5 in 8fko

Go back to Chlorine Binding Sites List in 8fko
Chlorine binding site 4 out of 5 in the Crystal Structure of HPK1 Kinase Domain T165E,S171E Phosphomimetic Mutant in Complex with 3-{4-[(2S,5R)-5-Amino-2-Methylpiperidin-1-Yl]- 6-Chloro-7H-Pyrrolo[2,3-D]Pyrimidin-5-Yl}Benzonitrile


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of HPK1 Kinase Domain T165E,S171E Phosphomimetic Mutant in Complex with 3-{4-[(2S,5R)-5-Amino-2-Methylpiperidin-1-Yl]- 6-Chloro-7H-Pyrrolo[2,3-D]Pyrimidin-5-Yl}Benzonitrile within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl401

b:54.7
occ:1.00
 CL1 D:Y3O401 0.0 54.7 1.0
C10 D:Y3O401 1.7 52.0 1.0
N2 D:Y3O401 2.7 51.0 1.0
C9 D:Y3O401 2.8 50.9 1.0
C8 D:Y3O401 3.3 50.7 1.0
C7 D:Y3O401 3.4 50.7 1.0
CE D:MET91 3.5 55.6 1.0
O D:HOH576 3.6 43.0 1.0
CG2 D:VAL75 3.7 45.8 1.0
CB D:MET91 3.7 48.6 1.0
SD D:MET91 3.8 60.6 1.0
C12 D:Y3O401 3.8 50.2 1.0
C13 D:Y3O401 3.9 50.0 1.0
O D:GLU92 3.9 47.0 1.0
CD1 D:LEU144 4.1 37.6 1.0
CB D:ALA44 4.3 49.9 1.0
CG D:MET91 4.4 51.7 1.0
C3 D:Y3O401 4.4 50.7 1.0
CB D:ALA154 4.5 33.6 1.0
C6 D:Y3O401 4.5 50.9 1.0
CG1 D:VAL75 4.5 46.1 1.0
CB D:VAL75 4.6 45.5 1.0

Chlorine binding site 5 out of 5 in 8fko

Go back to Chlorine Binding Sites List in 8fko
Chlorine binding site 5 out of 5 in the Crystal Structure of HPK1 Kinase Domain T165E,S171E Phosphomimetic Mutant in Complex with 3-{4-[(2S,5R)-5-Amino-2-Methylpiperidin-1-Yl]- 6-Chloro-7H-Pyrrolo[2,3-D]Pyrimidin-5-Yl}Benzonitrile


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of HPK1 Kinase Domain T165E,S171E Phosphomimetic Mutant in Complex with 3-{4-[(2S,5R)-5-Amino-2-Methylpiperidin-1-Yl]- 6-Chloro-7H-Pyrrolo[2,3-D]Pyrimidin-5-Yl}Benzonitrile within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl401

b:57.7
occ:1.00
 CL1 E:Y3O401 0.0 57.7 1.0
C10 E:Y3O401 1.7 54.0 1.0
N2 E:Y3O401 2.6 52.5 1.0
C9 E:Y3O401 2.8 52.2 1.0
CB E:MET91 3.2 60.5 1.0
SD E:MET91 3.3 74.9 1.0
C7 E:Y3O401 3.4 51.8 1.0
O E:HOH538 3.4 47.0 1.0
CE E:MET91 3.4 75.0 1.0
C8 E:Y3O401 3.4 51.8 1.0
CG E:MET91 3.8 65.1 1.0
C12 E:Y3O401 3.8 51.5 1.0
O E:GLU92 3.9 56.0 1.0
C13 E:Y3O401 4.0 51.0 1.0
CG2 E:VAL75 4.1 59.9 1.0
CG1 E:VAL75 4.2 59.9 1.0
CB E:ALA44 4.2 61.1 1.0
CD1 E:LEU144 4.4 38.0 1.0
C6 E:Y3O401 4.5 51.9 1.0
C3 E:Y3O401 4.6 51.3 1.0
CA E:MET91 4.6 58.9 1.0
CB E:ALA154 4.7 44.3 1.0
CB E:VAL75 4.7 59.5 1.0
C E:MET91 4.8 57.5 1.0
N E:GLU92 4.9 56.4 1.0

Reference:

R.A.Gallego, L.Bernier, H.Chen, S.Cho-Schultz, L.Chung, M.Collins, M.Del Bel, J.Elleraas, C.Costa Jones, C.N.Cronin, M.Edwards, X.Fang, T.Fisher, M.He, J.Hoffman, R.Huo, M.Jalaie, E.Johnson, T.W.Johnson, R.S.Kania, M.Kraus, J.Lafontaine, P.Le, T.Liu, M.Maestre, J.Matthews, M.Mctigue, N.Miller, Q.Mu, X.Qin, S.Ren, P.Richardson, A.Rohner, N.Sach, L.Shao, G.Smith, R.Su, B.Sun, S.Timofeevski, P.Tran, S.Wang, W.Wang, R.Zhou, J.Zhu, S.K.Nair. Design and Synthesis of Functionally Active 5-Amino-6-Aryl Pyrrolopyrimidine Inhibitors of Hematopoietic Progenitor Kinase 1. J.Med.Chem. 2023.
ISSN: ISSN 0022-2623
PubMed: 36940470
DOI: 10.1021/ACS.JMEDCHEM.2C02038
Page generated: Sun Jul 13 11:28:37 2025

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