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Chlorine in PDB 6npv: C-Abl Kinase Domain with the Activator(CMPD51), N-(1-(3,4- Dichlorophenyl)-4-(2-Hydroxyethyl)-4,5-Dihydro-1H-Pyrazol-3-Yl) Isonicotinamide

Enzymatic activity of C-Abl Kinase Domain with the Activator(CMPD51), N-(1-(3,4- Dichlorophenyl)-4-(2-Hydroxyethyl)-4,5-Dihydro-1H-Pyrazol-3-Yl) Isonicotinamide

All present enzymatic activity of C-Abl Kinase Domain with the Activator(CMPD51), N-(1-(3,4- Dichlorophenyl)-4-(2-Hydroxyethyl)-4,5-Dihydro-1H-Pyrazol-3-Yl) Isonicotinamide:
2.7.10.2;

Protein crystallography data

The structure of C-Abl Kinase Domain with the Activator(CMPD51), N-(1-(3,4- Dichlorophenyl)-4-(2-Hydroxyethyl)-4,5-Dihydro-1H-Pyrazol-3-Yl) Isonicotinamide, PDB code: 6npv was solved by N.Campobasso, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.72 / 1.86
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.973, 95.287, 115.361, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 20.7

Chlorine Binding Sites:

The binding sites of Chlorine atom in the C-Abl Kinase Domain with the Activator(CMPD51), N-(1-(3,4- Dichlorophenyl)-4-(2-Hydroxyethyl)-4,5-Dihydro-1H-Pyrazol-3-Yl) Isonicotinamide (pdb code 6npv). 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(CMPD51), N-(1-(3,4- Dichlorophenyl)-4-(2-Hydroxyethyl)-4,5-Dihydro-1H-Pyrazol-3-Yl) Isonicotinamide, PDB code: 6npv:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 6npv

Go back to Chlorine Binding Sites List in 6npv
Chlorine binding site 1 out of 4 in the C-Abl Kinase Domain with the Activator(CMPD51), N-(1-(3,4- Dichlorophenyl)-4-(2-Hydroxyethyl)-4,5-Dihydro-1H-Pyrazol-3-Yl) Isonicotinamide


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(CMPD51), N-(1-(3,4- Dichlorophenyl)-4-(2-Hydroxyethyl)-4,5-Dihydro-1H-Pyrazol-3-Yl) Isonicotinamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl603

b:22.2
occ:1.00
 CL24 A:KWP603 0.0 22.2 1.0
C10 A:KWP603 1.7 18.4 1.0
C11 A:KWP603 2.7 17.6 1.0
C2 A:KWP603 2.7 20.7 1.0
CL25 A:KWP603 3.1 25.1 1.0
CB A:ALA363 3.7 19.2 1.0
CA A:LEU360 3.7 17.0 1.0
O A:LEU359 3.8 16.0 1.0
CE1 A:PHE512 3.9 24.8 1.0
CG2 A:VAL487 3.9 21.7 1.0
CG1 A:VAL487 3.9 18.3 1.0
N A:LEU360 4.0 17.2 1.0
C5 A:KWP603 4.0 19.1 1.0
C1 A:KWP603 4.0 21.3 1.0
C A:LEU359 4.1 16.3 1.0
CD1 A:LEU360 4.2 28.1 1.0
CZ A:PHE512 4.4 24.4 1.0
CD2 A:LEU448 4.4 22.0 1.0
C9 A:KWP603 4.5 20.7 1.0
CB A:LEU360 4.5 18.1 1.0
CB A:VAL487 4.5 21.4 1.0
CD1 A:PHE512 4.8 24.6 1.0
C A:LEU360 4.8 16.9 1.0
CB A:LEU359 4.8 17.9 1.0
O A:LEU360 4.9 16.3 1.0
CG2 A:ILE451 4.9 16.5 1.0

Chlorine binding site 2 out of 4 in 6npv

Go back to Chlorine Binding Sites List in 6npv
Chlorine binding site 2 out of 4 in the C-Abl Kinase Domain with the Activator(CMPD51), N-(1-(3,4- Dichlorophenyl)-4-(2-Hydroxyethyl)-4,5-Dihydro-1H-Pyrazol-3-Yl) Isonicotinamide


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(CMPD51), N-(1-(3,4- Dichlorophenyl)-4-(2-Hydroxyethyl)-4,5-Dihydro-1H-Pyrazol-3-Yl) Isonicotinamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl603

b:25.1
occ:1.00
 CL25 A:KWP603 0.0 25.1 1.0
C11 A:KWP603 1.7 17.6 1.0
C10 A:KWP603 2.7 18.4 1.0
C5 A:KWP603 2.7 19.1 1.0
CL24 A:KWP603 3.1 22.2 1.0
O A:LEU448 3.2 14.7 1.0
CG2 A:ILE451 3.6 16.5 1.0
N A:ALA452 3.7 16.3 1.0
CB A:ALA452 3.8 18.1 1.0
CG1 A:VAL487 3.8 18.3 1.0
CB A:ILE451 3.9 14.9 1.0
CA A:ALA452 4.0 16.4 1.0
C2 A:KWP603 4.0 20.7 1.0
C9 A:KWP603 4.0 20.7 1.0
C A:LEU448 4.1 16.2 1.0
CD2 A:LEU448 4.2 22.0 1.0
C A:ILE451 4.3 17.6 1.0
CA A:LEU448 4.4 15.2 1.0
C1 A:KWP603 4.5 21.3 1.0
CB A:LEU448 4.5 17.9 1.0
CA A:ILE451 4.7 14.8 1.0
CE A:MET491 4.9 23.7 1.0
SG A:CYS483 4.9 26.2 1.0
CB A:VAL487 5.0 21.4 1.0
CG A:LEU448 5.0 20.0 1.0

Chlorine binding site 3 out of 4 in 6npv

Go back to Chlorine Binding Sites List in 6npv
Chlorine binding site 3 out of 4 in the C-Abl Kinase Domain with the Activator(CMPD51), N-(1-(3,4- Dichlorophenyl)-4-(2-Hydroxyethyl)-4,5-Dihydro-1H-Pyrazol-3-Yl) Isonicotinamide


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(CMPD51), N-(1-(3,4- Dichlorophenyl)-4-(2-Hydroxyethyl)-4,5-Dihydro-1H-Pyrazol-3-Yl) Isonicotinamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl607

b:19.2
occ:1.00
 CL24 B:KWP607 0.0 19.2 1.0
C10 B:KWP607 1.7 18.0 1.0
C11 B:KWP607 2.7 18.0 1.0
C2 B:KWP607 2.7 17.4 1.0
CL25 B:KWP607 3.0 24.4 1.0
CB B:ALA363 3.6 17.9 1.0
CA B:LEU360 3.8 13.5 1.0
CE1 B:PHE512 3.8 17.8 1.0
O B:LEU359 3.8 17.0 1.0
CD1 B:LEU360 3.9 22.7 1.0
C5 B:KWP607 4.0 15.6 1.0
C1 B:KWP607 4.0 18.7 1.0
CG2 B:VAL487 4.0 17.2 1.0
CG1 B:VAL487 4.1 17.5 1.0
N B:LEU360 4.1 16.4 1.0
C B:LEU359 4.1 17.7 1.0
CZ B:PHE512 4.5 16.3 1.0
CB B:LEU360 4.5 17.8 1.0
CD2 B:LEU448 4.5 16.8 1.0
C9 B:KWP607 4.5 16.4 1.0
CG2 B:ILE451 4.7 16.2 1.0
CB B:VAL487 4.7 16.5 1.0
CD1 B:PHE512 4.7 18.6 1.0
C B:LEU360 4.8 16.3 1.0
O B:LEU360 4.8 16.5 1.0
CG B:LEU360 4.9 22.7 1.0
CB B:LEU359 4.9 15.5 1.0
CA B:ALA363 5.0 17.3 1.0

Chlorine binding site 4 out of 4 in 6npv

Go back to Chlorine Binding Sites List in 6npv
Chlorine binding site 4 out of 4 in the C-Abl Kinase Domain with the Activator(CMPD51), N-(1-(3,4- Dichlorophenyl)-4-(2-Hydroxyethyl)-4,5-Dihydro-1H-Pyrazol-3-Yl) Isonicotinamide


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(CMPD51), N-(1-(3,4- Dichlorophenyl)-4-(2-Hydroxyethyl)-4,5-Dihydro-1H-Pyrazol-3-Yl) Isonicotinamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl607

b:24.4
occ:1.00
 CL25 B:KWP607 0.0 24.4 1.0
C11 B:KWP607 1.7 18.0 1.0
C10 B:KWP607 2.7 18.0 1.0
C5 B:KWP607 2.7 15.6 1.0
CL24 B:KWP607 3.0 19.2 1.0
O B:LEU448 3.2 15.2 1.0
CG2 B:ILE451 3.6 16.2 1.0
N B:ALA452 3.6 16.6 1.0
CG1 B:VAL487 3.7 17.5 1.0
CB B:ALA452 3.8 15.4 1.0
CB B:ILE451 3.8 15.1 1.0
CA B:ALA452 3.9 16.7 1.0
C2 B:KWP607 4.0 17.4 1.0
C9 B:KWP607 4.0 16.4 1.0
C B:LEU448 4.1 15.7 1.0
C B:ILE451 4.3 17.1 1.0
CA B:LEU448 4.3 16.3 1.0
CD2 B:LEU448 4.4 16.8 1.0
C1 B:KWP607 4.5 18.7 1.0
CB B:LEU448 4.5 13.5 1.0
CA B:ILE451 4.6 14.5 1.0
CE B:MET491 4.7 20.8 1.0
SG B:CYS483 4.8 21.2 1.0
CB B:VAL487 4.9 16.5 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: Mon Jul 29 12:09:17 2024

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