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Chlorine in PDB 6npu: C-Abl Kinase Domain with the Activator(CMPD29), N-(1-(3,4- Dichlorophenyl)-4,5-Dihydro-1H-Pyrazol-3-Yl)Acetamide

Enzymatic activity of C-Abl Kinase Domain with the Activator(CMPD29), N-(1-(3,4- Dichlorophenyl)-4,5-Dihydro-1H-Pyrazol-3-Yl)Acetamide

All present enzymatic activity of C-Abl Kinase Domain with the Activator(CMPD29), N-(1-(3,4- Dichlorophenyl)-4,5-Dihydro-1H-Pyrazol-3-Yl)Acetamide:
2.7.10.2;

Protein crystallography data

The structure of C-Abl Kinase Domain with the Activator(CMPD29), N-(1-(3,4- Dichlorophenyl)-4,5-Dihydro-1H-Pyrazol-3-Yl)Acetamide, PDB code: 6npu was solved by N.Campobasso, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 73.70 / 2.33
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 75.093, 95.643, 115.535, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 23.4

Chlorine Binding Sites:

The binding sites of Chlorine atom in the C-Abl Kinase Domain with the Activator(CMPD29), N-(1-(3,4- Dichlorophenyl)-4,5-Dihydro-1H-Pyrazol-3-Yl)Acetamide (pdb code 6npu). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the C-Abl Kinase Domain with the Activator(CMPD29), N-(1-(3,4- Dichlorophenyl)-4,5-Dihydro-1H-Pyrazol-3-Yl)Acetamide, PDB code: 6npu:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 6npu

Go back to Chlorine Binding Sites List in 6npu
Chlorine binding site 1 out of 4 in the C-Abl Kinase Domain with the Activator(CMPD29), N-(1-(3,4- Dichlorophenyl)-4,5-Dihydro-1H-Pyrazol-3-Yl)Acetamide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of C-Abl Kinase Domain with the Activator(CMPD29), N-(1-(3,4- Dichlorophenyl)-4,5-Dihydro-1H-Pyrazol-3-Yl)Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl602

b:29.5
occ:1.00
 CL14 A:KWV602 0.0 29.5 1.0
C13 A:KWV602 1.8 24.4 1.0
C15 A:KWV602 2.7 26.3 1.0
C12 A:KWV602 2.7 25.0 1.0
CL16 A:KWV602 3.1 38.9 1.0
CB A:ALA363 3.5 23.4 1.0
CE1 A:PHE512 3.7 28.5 1.0
CA A:LEU360 3.7 23.5 1.0
CG1 A:VAL487 3.8 24.3 1.0
CG2 A:VAL487 3.9 24.1 1.0
CD1 A:LEU360 3.9 25.6 1.0
O A:LEU359 4.0 20.4 1.0
C17 A:KWV602 4.0 25.7 1.0
C11 A:KWV602 4.0 23.5 1.0
N A:LEU360 4.1 22.1 1.0
CZ A:PHE512 4.2 25.9 1.0
C A:LEU359 4.3 22.9 1.0
CB A:VAL487 4.5 29.6 1.0
CB A:LEU360 4.5 20.6 1.0
C10 A:KWV602 4.5 23.8 1.0
CD1 A:PHE512 4.5 30.0 1.0
O A:LEU360 4.7 20.5 1.0
C A:LEU360 4.7 24.4 1.0
CG A:LEU360 4.9 26.9 1.0
CA A:ALA363 5.0 22.4 1.0

Chlorine binding site 2 out of 4 in 6npu

Go back to Chlorine Binding Sites List in 6npu
Chlorine binding site 2 out of 4 in the C-Abl Kinase Domain with the Activator(CMPD29), N-(1-(3,4- Dichlorophenyl)-4,5-Dihydro-1H-Pyrazol-3-Yl)Acetamide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of C-Abl Kinase Domain with the Activator(CMPD29), N-(1-(3,4- Dichlorophenyl)-4,5-Dihydro-1H-Pyrazol-3-Yl)Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl602

b:38.9
occ:1.00
 CL16 A:KWV602 0.0 38.9 1.0
C15 A:KWV602 1.8 26.3 1.0
C13 A:KWV602 2.8 24.4 1.0
C17 A:KWV602 2.8 25.7 1.0
CL14 A:KWV602 3.1 29.5 1.0
O A:LEU448 3.3 21.3 1.0
CG2 A:ILE451 3.7 19.9 1.0
CG1 A:VAL487 3.7 24.3 1.0
N A:ALA452 3.9 18.9 1.0
CB A:ILE451 4.0 21.4 1.0
CB A:ALA452 4.0 21.0 1.0
C12 A:KWV602 4.1 25.0 1.0
C10 A:KWV602 4.1 23.8 1.0
C A:LEU448 4.1 23.1 1.0
CA A:ALA452 4.3 21.8 1.0
CA A:LEU448 4.3 20.4 1.0
CG A:LEU448 4.4 23.9 1.0
CB A:LEU448 4.5 26.9 1.0
C A:ILE451 4.6 21.4 1.0
C11 A:KWV602 4.6 23.5 1.0
CA A:ILE451 4.8 19.0 1.0
CE A:MET491 5.0 29.5 1.0
CB A:ALA363 5.0 23.4 1.0
CB A:VAL487 5.0 29.6 1.0

Chlorine binding site 3 out of 4 in 6npu

Go back to Chlorine Binding Sites List in 6npu
Chlorine binding site 3 out of 4 in the C-Abl Kinase Domain with the Activator(CMPD29), N-(1-(3,4- Dichlorophenyl)-4,5-Dihydro-1H-Pyrazol-3-Yl)Acetamide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of C-Abl Kinase Domain with the Activator(CMPD29), N-(1-(3,4- Dichlorophenyl)-4,5-Dihydro-1H-Pyrazol-3-Yl)Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl605

b:25.0
occ:1.00
 CL14 B:KWV605 0.0 25.0 1.0
C13 B:KWV605 1.8 28.0 1.0
C15 B:KWV605 2.7 28.0 1.0
C12 B:KWV605 2.8 26.6 1.0
CL16 B:KWV605 3.1 42.5 1.0
CB B:ALA363 3.4 19.0 1.0
CE1 B:PHE512 3.5 25.1 1.0
CA B:LEU360 3.8 23.6 1.0
O B:LEU359 3.9 23.9 1.0
CD1 B:LEU360 3.9 26.7 1.0
CG2 B:VAL487 3.9 22.4 1.0
C17 B:KWV605 4.0 23.3 1.0
C11 B:KWV605 4.0 30.3 1.0
CG1 B:VAL487 4.1 21.9 1.0
CZ B:PHE512 4.1 25.3 1.0
N B:LEU360 4.2 23.7 1.0
C B:LEU359 4.2 27.0 1.0
CD1 B:PHE512 4.4 26.2 1.0
C10 B:KWV605 4.5 27.2 1.0
CB B:LEU360 4.5 23.6 1.0
CD2 B:LEU448 4.5 20.1 1.0
CB B:VAL487 4.7 25.7 1.0
O B:LEU360 4.7 22.9 1.0
C B:LEU360 4.8 23.0 1.0
CA B:ALA363 4.8 20.6 1.0
CG2 B:ILE451 4.8 22.3 1.0
CG B:LEU360 4.8 24.9 1.0

Chlorine binding site 4 out of 4 in 6npu

Go back to Chlorine Binding Sites List in 6npu
Chlorine binding site 4 out of 4 in the C-Abl Kinase Domain with the Activator(CMPD29), N-(1-(3,4- Dichlorophenyl)-4,5-Dihydro-1H-Pyrazol-3-Yl)Acetamide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of C-Abl Kinase Domain with the Activator(CMPD29), N-(1-(3,4- Dichlorophenyl)-4,5-Dihydro-1H-Pyrazol-3-Yl)Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl605

b:42.5
occ:1.00
 CL16 B:KWV605 0.0 42.5 1.0
C15 B:KWV605 1.8 28.0 1.0
C17 B:KWV605 2.7 23.3 1.0
C13 B:KWV605 2.8 28.0 1.0
CL14 B:KWV605 3.1 25.0 1.0
O B:LEU448 3.2 23.5 1.0
CG2 B:ILE451 3.6 22.3 1.0
CG1 B:VAL487 3.6 21.9 1.0
N B:ALA452 3.7 20.9 1.0
CB B:ALA452 3.9 19.3 1.0
CB B:ILE451 3.9 25.8 1.0
C B:LEU448 4.0 24.0 1.0
C10 B:KWV605 4.0 27.2 1.0
C12 B:KWV605 4.1 26.6 1.0
CA B:ALA452 4.1 26.1 1.0
CA B:LEU448 4.2 21.4 1.0
CB B:LEU448 4.3 18.9 1.0
C B:ILE451 4.4 23.8 1.0
CD2 B:LEU448 4.4 20.1 1.0
C11 B:KWV605 4.6 30.3 1.0
CA B:ILE451 4.7 24.5 1.0
CE B:MET491 4.7 21.8 1.0
CB B:VAL487 4.8 25.7 1.0
CG2 B:VAL487 5.0 22.4 1.0
CG B:LEU448 5.0 21.7 1.0

Reference:

G.L.Simpson, S.M.Bertrand, J.A.Borthwick, N.Campobasso, J.Chabanet, S.Chen, J.Coggins, J.Cottom, S.B.Christensen, H.C.Dawson, H.L.Evans, A.N.Hobbs, X.Hong, B.Mangatt, J.Munoz-Muriedas, A.Oliff, D.Qin, P.Scott-Stevens, P.Ward, Y.Washio, J.Yang, R.J.Young. Identification and Optimization of Novel Small C-Abl Kinase Activators Using Fragment and Hts Methodologies. J. Med. Chem. V. 62 2154 2019.
ISSN: ISSN 1520-4804
PubMed: 30689376
DOI: 10.1021/ACS.JMEDCHEM.8B01872
Page generated: Sat Jul 12 17:24:15 2025

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