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Chlorine in PDB 6d1y: Crystal Structure of Tyrosine-Protein Kinase Receptor in Complex with 2,4-Dichloro-N-(3-Methyl-1-Phenyl-1H-Pyrazol-5-Yl)Benzamide Inhibitor

Enzymatic activity of Crystal Structure of Tyrosine-Protein Kinase Receptor in Complex with 2,4-Dichloro-N-(3-Methyl-1-Phenyl-1H-Pyrazol-5-Yl)Benzamide Inhibitor

All present enzymatic activity of Crystal Structure of Tyrosine-Protein Kinase Receptor in Complex with 2,4-Dichloro-N-(3-Methyl-1-Phenyl-1H-Pyrazol-5-Yl)Benzamide Inhibitor:
2.7.10.1;

Protein crystallography data

The structure of Crystal Structure of Tyrosine-Protein Kinase Receptor in Complex with 2,4-Dichloro-N-(3-Methyl-1-Phenyl-1H-Pyrazol-5-Yl)Benzamide Inhibitor, PDB code: 6d1y was solved by S.E.Greasley, E.Johnson, M.L.Kraus, C.N.Cronin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 66.50 / 1.93
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 52.240, 48.551, 67.335, 90.00, 99.02, 90.00
R / Rfree (%) 17.7 / 22.4

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Tyrosine-Protein Kinase Receptor in Complex with 2,4-Dichloro-N-(3-Methyl-1-Phenyl-1H-Pyrazol-5-Yl)Benzamide Inhibitor (pdb code 6d1y). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Crystal Structure of Tyrosine-Protein Kinase Receptor in Complex with 2,4-Dichloro-N-(3-Methyl-1-Phenyl-1H-Pyrazol-5-Yl)Benzamide Inhibitor, PDB code: 6d1y:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 6d1y

Go back to Chlorine Binding Sites List in 6d1y
Chlorine binding site 1 out of 2 in the Crystal Structure of Tyrosine-Protein Kinase Receptor in Complex with 2,4-Dichloro-N-(3-Methyl-1-Phenyl-1H-Pyrazol-5-Yl)Benzamide Inhibitor


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 Tyrosine-Protein Kinase Receptor in Complex with 2,4-Dichloro-N-(3-Methyl-1-Phenyl-1H-Pyrazol-5-Yl)Benzamide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl801

b:26.1
occ:1.00
CL2 A:FQJ801 0.0 26.1 1.0
C8 A:FQJ801 1.7 18.9 1.0
C11 A:FQJ801 2.7 19.3 1.0
C7 A:FQJ801 2.7 15.4 1.0
H27 A:FQJ801 2.8 19.6 1.0
O13 A:FQJ801 3.1 14.5 1.0
C6 A:FQJ801 3.1 15.6 1.0
O A:HIS648 3.2 10.5 1.0
O A:HOH993 3.3 12.8 1.0
CD2 A:HIS648 3.6 12.0 1.0
CG A:HIS648 3.6 11.3 1.0
CA A:GLY485 3.6 10.1 1.0
NE2 A:HIS648 3.6 12.6 1.0
CE1 A:PHE646 3.7 14.3 1.0
CE1 A:HIS648 3.7 12.4 1.0
ND1 A:HIS648 3.7 12.9 1.0
N A:GLY485 3.8 9.6 1.0
CZ A:PHE646 3.8 12.8 1.0
CA A:HIS648 3.8 8.7 1.0
C A:HIS648 3.9 11.2 1.0
C14 A:FQJ801 3.9 19.9 1.0
C10 A:FQJ801 4.0 15.7 1.0
O A:HOH991 4.1 13.9 1.0
N5 A:FQJ801 4.2 16.9 1.0
C A:GLY485 4.2 12.4 1.0
N A:LEU486 4.2 11.5 1.0
CB A:HIS648 4.3 9.2 1.0
C16 A:FQJ801 4.5 16.1 1.0
H25 A:FQJ801 4.6 17.5 1.0
H26 A:FQJ801 4.9 15.6 1.0
O A:VAL647 4.9 10.5 1.0
CD1 A:PHE646 5.0 13.2 1.0

Chlorine binding site 2 out of 2 in 6d1y

Go back to Chlorine Binding Sites List in 6d1y
Chlorine binding site 2 out of 2 in the Crystal Structure of Tyrosine-Protein Kinase Receptor in Complex with 2,4-Dichloro-N-(3-Methyl-1-Phenyl-1H-Pyrazol-5-Yl)Benzamide Inhibitor


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 Tyrosine-Protein Kinase Receptor in Complex with 2,4-Dichloro-N-(3-Methyl-1-Phenyl-1H-Pyrazol-5-Yl)Benzamide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl801

b:27.9
occ:1.00
CL1 A:FQJ801 0.0 27.9 1.0
C14 A:FQJ801 1.7 19.9 1.0
C11 A:FQJ801 2.7 19.3 1.0
C16 A:FQJ801 2.7 16.1 1.0
H27 A:FQJ801 2.8 19.6 1.0
H28 A:FQJ801 2.8 16.4 1.0
CG2 A:ILE572 3.6 10.2 1.0
O A:ILE666 3.9 10.8 1.0
C8 A:FQJ801 4.0 18.9 1.0
C10 A:FQJ801 4.0 15.7 1.0
CD1 A:ILE572 4.1 17.0 1.0
C A:ILE666 4.3 10.4 1.0
CD1 A:LEU567 4.3 15.2 1.0
CG2 A:ILE666 4.4 12.7 1.0
O A:HOH963 4.4 23.3 1.0
CA A:GLY667 4.5 9.7 1.0
C7 A:FQJ801 4.5 15.4 1.0
N A:GLY667 4.6 10.0 1.0
O A:HOH910 4.7 9.6 1.0
CB A:ILE666 4.8 12.2 1.0
CB A:ILE572 4.8 11.0 1.0
H26 A:FQJ801 4.8 15.6 1.0
O A:HOH1020 4.9 14.4 1.0
CG1 A:ILE572 4.9 12.2 1.0
CD1 A:LEU641 4.9 11.0 1.0

Reference:

S.K.Bagal, K.Omoto, D.C.Blakemore, P.J.Bungay, J.G.Bilsland, P.J.Clarke, M.S.Corbett, C.N.Cronin, J.J.Cui, R.Dias, N.J.Flanagan, S.E.Greasley, R.Grimley, E.Johnson, D.Fengas, L.Kitching, M.L.Kraus, I.Mcalpine, A.Nagata, G.J.Waldron, J.S.Warmus. Discovery of Allosteric, Potent, Subtype Selective, and Peripherally Restricted Trka Kinase Inhibitors. J. Med. Chem. V. 62 247 2019.
ISSN: ISSN 1520-4804
PubMed: 29672039
DOI: 10.1021/ACS.JMEDCHEM.8B00280
Page generated: Sat Jul 12 12:38:47 2025

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