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Chlorine in PDB 5fp6: Structure of Cyclin-Dependent Kinase 2 with Small-Molecule Ligand 3-(4,7-Dichloro-1H-Indol-3-Yl)Prop-2-Yn-1-Ol (AT17833) in An Alternate Binding Site.

Enzymatic activity of Structure of Cyclin-Dependent Kinase 2 with Small-Molecule Ligand 3-(4,7-Dichloro-1H-Indol-3-Yl)Prop-2-Yn-1-Ol (AT17833) in An Alternate Binding Site.

All present enzymatic activity of Structure of Cyclin-Dependent Kinase 2 with Small-Molecule Ligand 3-(4,7-Dichloro-1H-Indol-3-Yl)Prop-2-Yn-1-Ol (AT17833) in An Alternate Binding Site.:
2.7.11.22;

Protein crystallography data

The structure of Structure of Cyclin-Dependent Kinase 2 with Small-Molecule Ligand 3-(4,7-Dichloro-1H-Indol-3-Yl)Prop-2-Yn-1-Ol (AT17833) in An Alternate Binding Site., PDB code: 5fp6 was solved by H.Jhoti, R.F.Ludlow, M.O'reilly, H.K.Saini, I.J.Tickle, M.Verdonk, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.29 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 53.917, 72.214, 72.198, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 24.03

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Structure of Cyclin-Dependent Kinase 2 with Small-Molecule Ligand 3-(4,7-Dichloro-1H-Indol-3-Yl)Prop-2-Yn-1-Ol (AT17833) in An Alternate Binding Site. (pdb code 5fp6). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Structure of Cyclin-Dependent Kinase 2 with Small-Molecule Ligand 3-(4,7-Dichloro-1H-Indol-3-Yl)Prop-2-Yn-1-Ol (AT17833) in An Alternate Binding Site., PDB code: 5fp6:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 5fp6

Go back to Chlorine Binding Sites List in 5fp6
Chlorine binding site 1 out of 4 in the Structure of Cyclin-Dependent Kinase 2 with Small-Molecule Ligand 3-(4,7-Dichloro-1H-Indol-3-Yl)Prop-2-Yn-1-Ol (AT17833) in An Alternate Binding Site.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of Cyclin-Dependent Kinase 2 with Small-Molecule Ligand 3-(4,7-Dichloro-1H-Indol-3-Yl)Prop-2-Yn-1-Ol (AT17833) in An Alternate Binding Site. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1295

b:26.9
occ:0.86
 CL1 A:MFZ1295 0.0 26.9 0.9
C10 A:MFZ1295 1.7 24.2 0.9
C12 A:MFZ1295 2.7 20.4 0.9
C9 A:MFZ1295 2.7 25.9 0.9
H12 A:MFZ1295 2.8 19.7 0.9
HN7 A:MFZ1295 3.0 25.6 0.9
N7 A:MFZ1295 3.2 24.6 0.9
O A:LEU83 3.2 22.4 1.0
N A:LEU83 3.3 20.1 1.0
CD1 A:LEU134 3.4 28.4 1.0
O A:HOH2123 3.5 47.8 1.0
CD1 A:PHE82 3.7 24.9 1.0
CD1 A:ILE10 3.8 29.9 1.0
CB A:ALA31 4.0 25.9 1.0
C13 A:MFZ1295 4.0 22.8 0.9
CA A:PHE82 4.0 22.2 1.0
C16 A:MFZ1295 4.1 26.6 0.9
C A:LEU83 4.1 24.1 1.0
C A:PHE82 4.2 22.8 1.0
CE1 A:PHE82 4.2 27.1 1.0
CA A:LEU83 4.2 19.9 1.0
O A:GLU81 4.3 21.8 1.0
CG A:PHE82 4.4 23.3 1.0
C14 A:MFZ1295 4.5 26.4 0.9
C6 A:MFZ1295 4.5 28.6 0.9
CD2 A:LEU134 4.5 33.4 1.0
CG A:LEU134 4.6 26.1 1.0
CB A:PHE82 4.6 22.9 1.0
CB A:LEU83 4.7 20.2 1.0
H13 A:MFZ1295 4.7 22.6 0.9
C5 A:MFZ1295 4.9 27.4 0.9

Chlorine binding site 2 out of 4 in 5fp6

Go back to Chlorine Binding Sites List in 5fp6
Chlorine binding site 2 out of 4 in the Structure of Cyclin-Dependent Kinase 2 with Small-Molecule Ligand 3-(4,7-Dichloro-1H-Indol-3-Yl)Prop-2-Yn-1-Ol (AT17833) in An Alternate Binding Site.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of Cyclin-Dependent Kinase 2 with Small-Molecule Ligand 3-(4,7-Dichloro-1H-Indol-3-Yl)Prop-2-Yn-1-Ol (AT17833) in An Alternate Binding Site. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1295

b:29.1
occ:0.86
 CL2 A:MFZ1295 0.0 29.1 0.9
C14 A:MFZ1295 1.7 26.4 0.9
C13 A:MFZ1295 2.7 22.8 0.9
C16 A:MFZ1295 2.8 26.6 0.9
H13 A:MFZ1295 2.8 22.6 0.9
C5 A:MFZ1295 3.4 27.4 0.9
OD1 A:ASP145 3.4 36.7 1.0
CB A:ASP145 3.5 27.5 1.0
O A:HOH2203 3.5 23.9 1.0
C4 A:MFZ1295 3.5 34.7 0.9
CA A:ASP145 3.7 24.6 1.0
CG A:ASP145 3.8 33.7 1.0
N A:ASP145 3.8 24.1 1.0
C12 A:MFZ1295 4.0 20.4 0.9
C3 A:MFZ1295 4.0 36.5 0.9
C9 A:MFZ1295 4.0 25.9 0.9
CD2 A:PHE80 4.1 24.1 1.0
CE2 A:PHE80 4.2 26.6 1.0
HO1 A:MFZ1295 4.3 37.7 0.9
CG2 A:VAL18 4.3 35.8 1.0
C10 A:MFZ1295 4.5 24.2 0.9
CG1 A:VAL18 4.5 34.7 1.0
CD A:LYS33 4.7 41.8 1.0
H12 A:MFZ1295 4.7 19.7 0.9
C6 A:MFZ1295 4.7 28.6 0.9
CG A:PHE80 4.8 21.4 1.0
CZ A:PHE80 4.8 25.2 1.0
CB A:ALA144 4.8 22.1 1.0
O1 A:MFZ1295 4.8 37.8 0.9
OD2 A:ASP145 4.8 47.8 1.0
C A:ALA144 4.8 24.3 1.0
C2 A:MFZ1295 5.0 37.3 0.9

Chlorine binding site 3 out of 4 in 5fp6

Go back to Chlorine Binding Sites List in 5fp6
Chlorine binding site 3 out of 4 in the Structure of Cyclin-Dependent Kinase 2 with Small-Molecule Ligand 3-(4,7-Dichloro-1H-Indol-3-Yl)Prop-2-Yn-1-Ol (AT17833) in An Alternate Binding Site.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of Cyclin-Dependent Kinase 2 with Small-Molecule Ligand 3-(4,7-Dichloro-1H-Indol-3-Yl)Prop-2-Yn-1-Ol (AT17833) in An Alternate Binding Site. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1296

b:42.1
occ:0.76
 CL1 A:MFZ1296 0.0 42.1 0.8
C10 A:MFZ1296 1.7 34.4 0.8
C12 A:MFZ1296 2.7 33.6 0.8
C9 A:MFZ1296 2.7 31.4 0.8
H12 A:MFZ1296 2.8 33.5 0.8
HN7 A:MFZ1296 3.1 33.0 0.8
N7 A:MFZ1296 3.3 32.8 0.8
O A:HOH2067 3.6 53.8 1.0
CB A:PRO45 3.7 30.9 1.0
O A:THR41 3.7 37.5 1.0
CD1 A:LEU37 3.7 35.1 1.0
CA A:GLU42 3.8 36.4 1.0
OG1 A:THR41 3.8 50.9 1.0
CG A:GLU42 3.9 42.2 1.0
C13 A:MFZ1296 4.0 30.7 0.8
C16 A:MFZ1296 4.0 28.2 0.8
C A:THR41 4.1 38.9 1.0
N A:GLU42 4.1 36.0 1.0
NE2 A:HIS71 4.3 30.7 1.0
CE1 A:HIS71 4.4 31.1 1.0
CB A:GLU42 4.4 37.7 1.0
CD2 A:LEU37 4.4 38.5 1.0
C14 A:MFZ1296 4.5 29.6 0.8
CG A:LEU37 4.6 35.9 1.0
CA A:PRO45 4.6 28.9 1.0
C6 A:MFZ1296 4.6 32.4 0.8
H13 A:MFZ1296 4.7 30.6 0.8
CG A:PRO45 4.8 33.4 1.0
CD2 A:HIS71 4.8 30.5 1.0
C A:GLU42 4.8 39.7 1.0
O A:GLU42 4.8 39.5 1.0
ND1 A:HIS71 4.9 32.2 1.0
OE2 A:GLU42 4.9 45.9 1.0
CD A:GLU42 4.9 56.9 1.0
C5 A:MFZ1296 5.0 30.7 0.8
CB A:THR41 5.0 46.9 1.0

Chlorine binding site 4 out of 4 in 5fp6

Go back to Chlorine Binding Sites List in 5fp6
Chlorine binding site 4 out of 4 in the Structure of Cyclin-Dependent Kinase 2 with Small-Molecule Ligand 3-(4,7-Dichloro-1H-Indol-3-Yl)Prop-2-Yn-1-Ol (AT17833) in An Alternate Binding Site.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structure of Cyclin-Dependent Kinase 2 with Small-Molecule Ligand 3-(4,7-Dichloro-1H-Indol-3-Yl)Prop-2-Yn-1-Ol (AT17833) in An Alternate Binding Site. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1296

b:30.4
occ:0.76
 CL2 A:MFZ1296 0.0 30.4 0.8
C14 A:MFZ1296 1.7 29.6 0.8
C13 A:MFZ1296 2.7 30.7 0.8
C16 A:MFZ1296 2.7 28.2 0.8
H13 A:MFZ1296 2.8 30.6 0.8
C4 A:MFZ1296 3.2 32.2 0.8
HO1 A:MFZ1296 3.2 45.4 0.8
C5 A:MFZ1296 3.3 30.7 0.8
C3 A:MFZ1296 3.5 36.7 0.8
CG2 A:ILE52 3.8 32.6 1.0
CB A:ILE52 3.9 31.5 1.0
CG1 A:ILE49 3.9 26.8 1.0
CG1 A:VAL69 3.9 25.0 1.0
C12 A:MFZ1296 4.0 33.6 0.8
CA A:ILE49 4.0 26.1 1.0
C9 A:MFZ1296 4.0 31.4 0.8
CD1 A:LEU76 4.0 29.0 1.0
O1 A:MFZ1296 4.0 45.1 0.8
CD2 A:LEU76 4.1 32.3 1.0
CG1 A:ILE52 4.2 31.9 1.0
C2 A:MFZ1296 4.4 43.2 0.8
CB A:ILE49 4.5 27.9 1.0
O A:ALA48 4.5 30.1 1.0
C10 A:MFZ1296 4.5 34.4 0.8
N A:ILE49 4.5 28.3 1.0
C6 A:MFZ1296 4.6 32.4 0.8
CG A:LEU76 4.7 29.9 1.0
H12 A:MFZ1296 4.7 33.5 0.8
C A:ALA48 4.7 32.6 1.0
N7 A:MFZ1296 5.0 32.8 0.8
CG2 A:ILE49 5.0 28.2 1.0
O A:ILE49 5.0 28.1 1.0

Reference:

R.F.Ludlow, M.L.Verdonk, H.K.Saini, I.J.Tickle, H.Jhoti. Detection of Secondary Binding Sites in Proteins Using Fragment Screening. Proc.Natl.Acad.Sci.Usa V. 112 15910 2015.
ISSN: ISSN 0027-8424
PubMed: 26655740
DOI: 10.1073/PNAS.1518946112
Page generated: Fri Jul 26 08:06:58 2024

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