Atomistry » Chlorine » PDB 5aaa-5afy » 5ack
Atomistry »
  Chlorine »
    PDB 5aaa-5afy »
      5ack »

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: Fri Jul 26 05:06:19 2024

Last articles

Cl in 3QQH
Cl in 3QQ0
Cl in 3QQG
Cl in 3QPY
Cl in 3QQ8
Cl in 3QQ7
Cl in 3QP5
Cl in 3QPX
Cl in 3QPJ
Cl in 3QPK
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy