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Chlorine in PDB 5ack: Human PDK1 Kinase Domain in Complex with Allosteric Compound 7 Bound to the Pif-Pocket

Enzymatic activity of Human PDK1 Kinase Domain in Complex with Allosteric Compound 7 Bound to the Pif-Pocket

All present enzymatic activity of Human PDK1 Kinase Domain in Complex with Allosteric Compound 7 Bound to the Pif-Pocket:
2.7.11.1;

Protein crystallography data

The structure of Human PDK1 Kinase Domain in Complex with Allosteric Compound 7 Bound to the Pif-Pocket, PDB code: 5ack was solved by J.O.Schulze, E.Kroon, A.Doemling, R.M.Biondi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 72.568 / 1.24
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 147.980, 44.540, 47.810, 90.00, 101.25, 90.00
R / Rfree (%) 14.16 / 16.55

Other elements in 5ack:

The structure of Human PDK1 Kinase Domain in Complex with Allosteric Compound 7 Bound to the Pif-Pocket also contains other interesting chemical elements:

Sodium (Na) 4 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Human PDK1 Kinase Domain in Complex with Allosteric Compound 7 Bound to the Pif-Pocket (pdb code 5ack). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Human PDK1 Kinase Domain in Complex with Allosteric Compound 7 Bound to the Pif-Pocket, PDB code: 5ack:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 5ack

Go back to Chlorine Binding Sites List in 5ack
Chlorine binding site 1 out of 4 in the Human PDK1 Kinase Domain in Complex with Allosteric Compound 7 Bound to the Pif-Pocket


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Human PDK1 Kinase Domain in Complex with Allosteric Compound 7 Bound to the Pif-Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl600

b:41.7
occ:0.53
CL2 A:SVQ600 0.0 41.7 0.5
C23 A:SVQ600 0.7 34.3 0.5
C22 A:SVQ600 1.4 34.8 0.5
C25 A:SVQ600 1.8 37.5 0.5
C24 A:SVQ600 2.0 34.7 0.5
HG13 A:VAL127 2.5 32.4 0.5
C21 A:SVQ600 2.6 35.5 0.5
C24 A:SVQ600 2.7 34.0 0.5
C20 A:SVQ600 2.9 35.9 0.5
C25 A:SVQ600 2.9 36.6 0.5
C20 A:SVQ600 3.1 36.1 0.5
HA A:THR128 3.2 23.6 1.0
C14 A:SVQ600 3.3 37.2 0.5
HB2 A:ARG131 3.4 20.8 1.0
CG1 A:VAL127 3.4 27.0 0.5
HG21 A:VAL127 3.5 21.2 0.5
O A:VAL127 3.5 19.9 1.0
HG12 A:VAL127 3.6 32.4 0.5
HB3 A:ARG131 3.7 20.8 1.0
HZ A:PHE157 3.7 25.1 1.0
HG11 A:VAL127 3.8 32.4 0.5
C A:VAL127 3.8 19.6 1.0
CD A:ARG131 3.9 22.9 1.0
CB A:ARG131 3.9 17.4 1.0
HB A:VAL127 3.9 23.3 0.5
C23 A:SVQ600 4.0 32.1 0.5
CA A:THR128 4.0 19.6 1.0
N A:THR128 4.1 19.3 1.0
C21 A:SVQ600 4.1 34.1 0.5
C13 A:SVQ600 4.2 40.2 0.5
C8 A:SVQ600 4.2 33.5 0.5
C17 A:SVQ600 4.3 43.0 0.5
CG2 A:VAL127 4.3 17.7 0.5
HB A:VAL127 4.3 30.2 0.5
CZ A:PHE157 4.3 21.0 1.0
O19 A:SVQ600 4.3 43.9 0.5
HD23 A:LEU155 4.4 27.9 1.0
CB A:VAL127 4.4 25.1 0.5
N9 A:SVQ600 4.4 35.6 0.5
HD11 A:LEU155 4.4 34.8 1.0
HG22 A:VAL127 4.5 21.2 0.5
CB A:VAL127 4.5 19.4 0.5
CG A:ARG131 4.5 19.6 1.0
CL2 A:SVQ600 4.5 37.6 0.5
C22 A:SVQ600 4.6 32.9 0.5
H A:THR128 4.6 23.2 1.0
H A:ARG131 4.6 19.5 1.0
C14 A:SVQ600 4.6 37.5 0.5
HG1 A:THR128 4.7 31.3 1.0
OG1 A:THR128 4.7 26.1 1.0
C1 A:SVQ600 4.7 30.3 0.5
CA A:VAL127 4.7 21.0 0.5
O A:HOH2061 4.8 40.1 1.0
CA A:VAL127 4.8 19.2 0.5
O18 A:SVQ600 4.8 44.4 0.5
HE1 A:PHE157 4.8 25.4 1.0
HG21 A:THR128 4.8 29.7 1.0
C7 A:SVQ600 4.8 32.1 0.5
CE1 A:PHE157 4.9 21.2 1.0
C1 A:SVQ600 4.9 29.7 0.5
CB A:THR128 5.0 23.4 1.0
HE2 A:PHE157 5.0 24.2 1.0
C A:THR128 5.0 18.7 1.0

Chlorine binding site 2 out of 4 in 5ack

Go back to Chlorine Binding Sites List in 5ack
Chlorine binding site 2 out of 4 in the Human PDK1 Kinase Domain in Complex with Allosteric Compound 7 Bound to the Pif-Pocket


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Human PDK1 Kinase Domain in Complex with Allosteric Compound 7 Bound to the Pif-Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl600

b:33.3
occ:0.53
CL1 A:SVQ600 0.0 33.3 0.5
CL1 A:SVQ600 0.6 34.9 0.5
C5 A:SVQ600 1.8 31.2 0.5
C5 A:SVQ600 2.2 32.2 0.5
C4 A:SVQ600 2.8 30.0 0.5
C6 A:SVQ600 2.8 29.9 0.5
HA A:LYS115 2.9 31.2 1.0
HG13 A:ILE119 2.9 42.2 1.0
HB A:ILE118 3.0 33.9 1.0
C6 A:SVQ600 3.0 30.5 0.5
HB3 A:LYS115 3.1 30.7 1.0
HG2 A:LYS115 3.1 30.6 1.0
C4 A:SVQ600 3.2 31.0 0.5
HG23 A:VAL124 3.2 33.5 1.0
HG22 A:ILE118 3.4 35.3 1.0
O A:LYS115 3.4 29.8 1.0
HG23 A:ILE118 3.5 35.3 1.0
HD12 A:LEU155 3.5 34.8 1.0
HD12 A:ILE119 3.5 42.1 1.0
CA A:LYS115 3.5 26.0 1.0
CB A:LYS115 3.6 25.6 1.0
CG2 A:ILE118 3.7 29.4 1.0
CG1 A:ILE119 3.7 35.2 1.0
CB A:ILE118 3.7 28.2 1.0
CG A:LYS115 3.8 25.5 1.0
HD13 A:ILE119 3.8 42.1 1.0
C A:LYS115 3.9 28.9 1.0
CD1 A:ILE119 3.9 35.1 1.0
H A:ILE119 4.0 36.3 1.0
C3 A:SVQ600 4.0 29.6 0.5
C1 A:SVQ600 4.0 29.7 0.5
CG2 A:VAL124 4.1 27.9 1.0
HG12 A:ILE119 4.1 42.2 1.0
HG22 A:VAL124 4.2 33.5 1.0
C1 A:SVQ600 4.3 30.3 0.5
N A:ILE119 4.3 30.2 1.0
CD1 A:LEU155 4.4 29.0 1.0
HG13 A:ILE118 4.4 35.5 1.0
HG21 A:VAL124 4.4 33.5 1.0
HD3 A:LYS115 4.5 30.9 1.0
C3 A:SVQ600 4.5 30.4 0.5
HB2 A:LYS115 4.5 30.7 1.0
HD13 A:LEU155 4.5 34.8 1.0
HG3 A:LYS115 4.5 30.6 1.0
C2 A:SVQ600 4.5 30.6 0.5
CG1 A:ILE118 4.6 29.6 1.0
HG21 A:ILE118 4.7 35.3 1.0
HE2 A:LYS115 4.7 32.3 1.0
CD A:LYS115 4.7 25.7 1.0
HD22 A:LEU155 4.8 27.9 1.0
C A:ILE118 4.8 29.8 1.0
HG11 A:VAL124 4.8 32.6 1.0
CA A:ILE118 4.8 29.4 1.0
N A:LYS115 4.8 24.8 1.0
HD11 A:ILE119 4.8 42.1 1.0
HG22 A:VAL127 4.8 21.2 0.5
HG12 A:ILE118 4.9 35.5 1.0
CB A:ILE119 4.9 34.4 1.0
HG A:LEU155 4.9 28.8 1.0
HA A:ILE119 4.9 39.7 1.0
C2 A:SVQ600 4.9 30.9 0.5
H A:ILE118 4.9 37.0 1.0
HA A:VAL124 4.9 29.3 1.0
HD11 A:LEU155 5.0 34.8 1.0

Chlorine binding site 3 out of 4 in 5ack

Go back to Chlorine Binding Sites List in 5ack
Chlorine binding site 3 out of 4 in the Human PDK1 Kinase Domain in Complex with Allosteric Compound 7 Bound to the Pif-Pocket


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Human PDK1 Kinase Domain in Complex with Allosteric Compound 7 Bound to the Pif-Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl600

b:37.6
occ:0.47
CL2 A:SVQ600 0.0 37.6 0.5
C22 A:SVQ600 0.8 32.9 0.5
C23 A:SVQ600 0.9 32.1 0.5
C25 A:SVQ600 1.8 36.6 0.5
C21 A:SVQ600 2.1 34.1 0.5
C24 A:SVQ600 2.1 34.0 0.5
C24 A:SVQ600 2.7 34.7 0.5
C25 A:SVQ600 2.8 37.5 0.5
C20 A:SVQ600 2.8 35.9 0.5
C20 A:SVQ600 2.8 36.1 0.5
HB A:THR148 2.9 23.9 1.0
HD23 A:LEU155 3.1 27.9 1.0
O A:PHE149 3.1 19.9 1.0
C14 A:SVQ600 3.2 37.5 0.5
HB3 A:LEU155 3.3 25.3 1.0
HB3 A:GLN150 3.3 29.4 1.0
H A:TYR156 3.4 19.9 1.0
HD21 A:LEU155 3.6 27.9 1.0
H A:PHE149 3.6 23.1 1.0
C A:PHE149 3.7 19.5 1.0
HA A:LEU155 3.7 23.1 1.0
CD2 A:LEU155 3.8 23.2 1.0
C17 A:SVQ600 3.8 42.4 0.5
C13 A:SVQ600 3.8 40.3 0.5
CB A:THR148 3.9 19.9 1.0
N A:PHE149 3.9 19.2 1.0
O19 A:SVQ600 4.0 42.0 0.5
C23 A:SVQ600 4.0 34.3 0.5
O A:TYR156 4.0 16.0 1.0
CB A:LEU155 4.1 21.1 1.0
N A:TYR156 4.1 16.5 1.0
C21 A:SVQ600 4.1 35.5 0.5
HA A:PHE149 4.2 24.2 1.0
CA A:PHE149 4.2 20.2 1.0
C14 A:SVQ600 4.3 37.2 0.5
HG1 A:THR148 4.3 27.3 1.0
CB A:GLN150 4.3 24.5 1.0
O18 A:SVQ600 4.3 43.5 0.5
CA A:LEU155 4.3 19.3 1.0
OG1 A:THR148 4.4 22.8 1.0
N A:GLN150 4.4 22.0 1.0
N9 A:SVQ600 4.4 36.2 0.5
HD22 A:LEU155 4.5 27.9 1.0
C A:THR148 4.5 19.8 1.0
HG22 A:THR148 4.5 24.7 1.0
CL2 A:SVQ600 4.5 41.7 0.5
C8 A:SVQ600 4.5 33.6 0.5
CG A:LEU155 4.6 24.0 1.0
C22 A:SVQ600 4.6 34.8 0.5
HA A:GLN150 4.6 27.7 1.0
CG2 A:THR148 4.6 20.6 1.0
C A:LEU155 4.7 17.2 1.0
N9 A:SVQ600 4.7 35.6 0.5
CA A:THR148 4.7 18.5 1.0
HG23 A:THR148 4.7 24.7 1.0
CA A:GLN150 4.7 23.1 1.0
C8 A:SVQ600 4.8 33.5 0.5
HA A:THR148 4.8 22.2 1.0
C A:TYR156 4.8 15.7 1.0
HB2 A:GLN150 4.8 29.4 1.0
HG2 A:GLN150 4.8 33.3 1.0
HB2 A:LEU155 4.9 25.3 1.0
C13 A:SVQ600 4.9 40.2 0.5
HD11 A:LEU155 5.0 34.8 1.0

Chlorine binding site 4 out of 4 in 5ack

Go back to Chlorine Binding Sites List in 5ack
Chlorine binding site 4 out of 4 in the Human PDK1 Kinase Domain in Complex with Allosteric Compound 7 Bound to the Pif-Pocket


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Human PDK1 Kinase Domain in Complex with Allosteric Compound 7 Bound to the Pif-Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl600

b:34.9
occ:0.47
CL1 A:SVQ600 0.0 34.9 0.5
CL1 A:SVQ600 0.6 33.3 0.5
C5 A:SVQ600 1.4 31.2 0.5
C5 A:SVQ600 1.8 32.2 0.5
C4 A:SVQ600 2.3 30.0 0.5
C6 A:SVQ600 2.6 29.9 0.5
C4 A:SVQ600 2.7 31.0 0.5
C6 A:SVQ600 2.8 30.5 0.5
HG13 A:ILE119 3.0 42.2 1.0
HB3 A:LYS115 3.1 30.7 1.0
HG23 A:VAL124 3.2 33.5 1.0
HG2 A:LYS115 3.2 30.6 1.0
HD12 A:ILE119 3.2 42.1 1.0
HA A:LYS115 3.4 31.2 1.0
HB A:ILE118 3.6 33.9 1.0
C3 A:SVQ600 3.6 29.6 0.5
HD12 A:LEU155 3.7 34.8 1.0
CG1 A:ILE119 3.7 35.2 1.0
C1 A:SVQ600 3.8 29.7 0.5
CB A:LYS115 3.8 25.6 1.0
CD1 A:ILE119 3.8 35.1 1.0
HG22 A:ILE118 3.8 35.3 1.0
O A:LYS115 3.8 29.8 1.0
HD13 A:ILE119 3.8 42.1 1.0
HG23 A:ILE118 3.9 35.3 1.0
CG A:LYS115 3.9 25.5 1.0
CA A:LYS115 3.9 26.0 1.0
HG12 A:ILE119 4.0 42.2 1.0
C3 A:SVQ600 4.0 30.4 0.5
CG2 A:VAL124 4.0 27.9 1.0
C1 A:SVQ600 4.0 30.3 0.5
HG22 A:VAL124 4.0 33.5 1.0
C2 A:SVQ600 4.1 30.6 0.5
CG2 A:ILE118 4.2 29.4 1.0
C A:LYS115 4.3 28.9 1.0
HD3 A:LYS115 4.3 30.9 1.0
CB A:ILE118 4.3 28.2 1.0
H A:ILE119 4.4 36.3 1.0
HG21 A:VAL124 4.5 33.5 1.0
HE2 A:LYS115 4.5 32.3 1.0
C2 A:SVQ600 4.6 30.9 0.5
HG11 A:VAL124 4.6 32.6 1.0
CD1 A:LEU155 4.6 29.0 1.0
CD A:LYS115 4.6 25.7 1.0
HB2 A:LYS115 4.7 30.7 1.0
HD11 A:ILE119 4.7 42.1 1.0
HG3 A:LYS115 4.7 30.6 1.0
HD22 A:LEU155 4.7 27.9 1.0
N A:ILE119 4.7 30.2 1.0
HD13 A:LEU155 4.8 34.8 1.0
HG13 A:ILE118 4.9 35.5 1.0
CB A:ILE119 5.0 34.4 1.0

Reference:

E.Kroon, J.O.Schulze, E.Suss, C.J.Camacho, R.M.Biondi, A.Domling. Discovery of A Potent Allosteric Kinase Modulator By Combining Computational and Synthetic Methods. Angew.Chem.Int.Ed.Engl. V. 54 13933 2015.
ISSN: ISSN 1433-7851
PubMed: 26385475
DOI: 10.1002/ANIE.201506310
Page generated: Sat Jul 12 00:07:43 2025

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