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Fluorine in PDB 4zji: PAK1 in Complex with 2-Chloro-5-Ethyl-8-Fluoro-11-(4-Methylpiperazin- 1-Yl)-Dibenzodiazepine

Enzymatic activity of PAK1 in Complex with 2-Chloro-5-Ethyl-8-Fluoro-11-(4-Methylpiperazin- 1-Yl)-Dibenzodiazepine

All present enzymatic activity of PAK1 in Complex with 2-Chloro-5-Ethyl-8-Fluoro-11-(4-Methylpiperazin- 1-Yl)-Dibenzodiazepine:
2.7.11.1;

Protein crystallography data

The structure of PAK1 in Complex with 2-Chloro-5-Ethyl-8-Fluoro-11-(4-Methylpiperazin- 1-Yl)-Dibenzodiazepine, PDB code: 4zji was solved by S.Gutmann, G.Rummel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 81.81 / 1.99
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 110.520, 115.060, 116.360, 90.00, 90.00, 90.00
R / Rfree (%) 19.1 / 22

Other elements in 4zji:

The structure of PAK1 in Complex with 2-Chloro-5-Ethyl-8-Fluoro-11-(4-Methylpiperazin- 1-Yl)-Dibenzodiazepine also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Chlorine (Cl) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the PAK1 in Complex with 2-Chloro-5-Ethyl-8-Fluoro-11-(4-Methylpiperazin- 1-Yl)-Dibenzodiazepine (pdb code 4zji). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the PAK1 in Complex with 2-Chloro-5-Ethyl-8-Fluoro-11-(4-Methylpiperazin- 1-Yl)-Dibenzodiazepine, PDB code: 4zji:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 4zji

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Fluorine binding site 1 out of 4 in the PAK1 in Complex with 2-Chloro-5-Ethyl-8-Fluoro-11-(4-Methylpiperazin- 1-Yl)-Dibenzodiazepine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of PAK1 in Complex with 2-Chloro-5-Ethyl-8-Fluoro-11-(4-Methylpiperazin- 1-Yl)-Dibenzodiazepine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:23.1
occ:1.00
 F A:4OQ601 0.0 23.1 1.0
C5 A:4OQ601 1.4 25.6 1.0
C6 A:4OQ601 2.3 23.9 1.0
C4 A:4OQ601 2.3 23.3 1.0
NE2 A:HIS387 3.1 19.4 1.0
CD2 A:HIS387 3.1 19.1 1.0
C A:THR406 3.2 20.7 1.0
O A:THR406 3.3 19.7 1.0
CG A:LEU405 3.5 23.3 1.0
C3 A:4OQ601 3.6 21.8 1.0
C7 A:4OQ601 3.6 23.6 1.0
N A:ASP407 3.6 18.0 1.0
CB A:ASP407 3.7 19.7 1.0
CA A:THR406 3.7 17.5 1.0
N A:THR406 3.8 17.9 1.0
O A:LEU405 3.9 20.8 1.0
C A:LEU405 3.9 22.0 1.0
CD2 A:LEU405 4.0 22.5 1.0
C2 A:4OQ601 4.1 21.6 1.0
CA A:ASP407 4.1 18.3 1.0
CB A:LEU405 4.3 18.7 1.0
CD1 A:LEU405 4.3 23.4 1.0
CD1 A:LEU380 4.4 20.1 1.0
CE1 A:HIS387 4.4 19.1 1.0
CG A:HIS387 4.4 18.7 1.0
N1 A:4OQ601 4.7 23.7 1.0
CA A:LEU405 4.8 18.5 1.0
O A:HOH861 4.8 23.8 1.0
CG A:ASP407 4.9 21.9 1.0
CG2 A:ILE327 5.0 19.1 1.0

Fluorine binding site 2 out of 4 in 4zji

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Fluorine binding site 2 out of 4 in the PAK1 in Complex with 2-Chloro-5-Ethyl-8-Fluoro-11-(4-Methylpiperazin- 1-Yl)-Dibenzodiazepine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of PAK1 in Complex with 2-Chloro-5-Ethyl-8-Fluoro-11-(4-Methylpiperazin- 1-Yl)-Dibenzodiazepine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F601

b:30.4
occ:1.00
 F B:4OQ601 0.0 30.4 1.0
C5 B:4OQ601 1.4 30.4 1.0
C6 B:4OQ601 2.3 29.7 1.0
C4 B:4OQ601 2.4 28.9 1.0
NE2 B:HIS387 3.1 22.5 1.0
CD2 B:HIS387 3.1 22.8 1.0
C B:THR406 3.2 25.5 1.0
O B:THR406 3.3 24.7 1.0
N B:ASP407 3.6 21.6 1.0
CG B:LEU405 3.6 28.4 1.0
C3 B:4OQ601 3.6 28.9 1.0
C7 B:4OQ601 3.6 30.5 1.0
CB B:ASP407 3.6 24.0 1.0
CA B:THR406 3.7 23.2 1.0
N B:THR406 3.9 23.1 1.0
O B:LEU405 3.9 26.2 1.0
C B:LEU405 3.9 26.7 1.0
CD2 B:LEU405 4.1 27.7 1.0
CA B:ASP407 4.1 22.1 1.0
C2 B:4OQ601 4.1 29.6 1.0
CD1 B:LEU380 4.4 24.5 1.0
CE1 B:HIS387 4.4 21.8 1.0
CD1 B:LEU405 4.4 27.6 1.0
CB B:LEU405 4.4 23.7 1.0
CG B:HIS387 4.4 21.9 1.0
N1 B:4OQ601 4.7 29.0 1.0
O B:HOH826 4.8 29.0 1.0
CA B:LEU405 4.8 23.4 1.0
CG B:ASP407 4.9 26.3 1.0
CG2 B:ILE327 5.0 28.6 1.0

Fluorine binding site 3 out of 4 in 4zji

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Fluorine binding site 3 out of 4 in the PAK1 in Complex with 2-Chloro-5-Ethyl-8-Fluoro-11-(4-Methylpiperazin- 1-Yl)-Dibenzodiazepine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of PAK1 in Complex with 2-Chloro-5-Ethyl-8-Fluoro-11-(4-Methylpiperazin- 1-Yl)-Dibenzodiazepine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F601

b:28.7
occ:1.00
 F C:4OQ601 0.0 28.7 1.0
C5 C:4OQ601 1.4 29.2 1.0
C4 C:4OQ601 2.3 29.1 1.0
C6 C:4OQ601 2.3 28.0 1.0
NE2 C:HIS387 3.1 25.5 1.0
CD2 C:HIS387 3.1 25.8 1.0
O C:THR406 3.2 25.2 1.0
C C:THR406 3.2 26.8 1.0
CG C:LEU405 3.6 28.0 1.0
C3 C:4OQ601 3.6 27.4 1.0
N C:ASP407 3.6 27.0 1.0
C7 C:4OQ601 3.6 31.2 1.0
CA C:THR406 3.8 23.4 1.0
CB C:ASP407 3.8 30.6 1.0
O C:LEU405 3.9 25.0 1.0
N C:THR406 3.9 22.7 1.0
C C:LEU405 3.9 26.7 1.0
CD2 C:LEU405 4.0 28.0 1.0
C2 C:4OQ601 4.1 28.0 1.0
CA C:ASP407 4.1 28.4 1.0
CD1 C:LEU380 4.3 25.4 1.0
CE1 C:HIS387 4.4 25.2 1.0
CB C:LEU405 4.4 23.4 1.0
CD1 C:LEU405 4.4 27.9 1.0
CG C:HIS387 4.4 24.4 1.0
N1 C:4OQ601 4.7 30.6 1.0
CA C:LEU405 4.8 22.9 1.0
O C:HOH825 4.8 34.8 1.0
CG2 C:ILE327 4.9 24.9 1.0
CG C:ASP407 4.9 40.1 1.0

Fluorine binding site 4 out of 4 in 4zji

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Fluorine binding site 4 out of 4 in the PAK1 in Complex with 2-Chloro-5-Ethyl-8-Fluoro-11-(4-Methylpiperazin- 1-Yl)-Dibenzodiazepine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of PAK1 in Complex with 2-Chloro-5-Ethyl-8-Fluoro-11-(4-Methylpiperazin- 1-Yl)-Dibenzodiazepine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F601

b:26.8
occ:1.00
 F D:4OQ601 0.0 26.8 1.0
C5 D:4OQ601 1.4 27.1 1.0
C4 D:4OQ601 2.3 26.6 1.0
C6 D:4OQ601 2.3 25.1 1.0
CD2 D:HIS387 3.1 25.4 1.0
NE2 D:HIS387 3.1 25.0 1.0
O D:THR406 3.3 22.7 1.0
C D:THR406 3.3 26.4 1.0
CG D:LEU405 3.6 24.0 1.0
C3 D:4OQ601 3.6 26.3 1.0
C7 D:4OQ601 3.6 27.6 1.0
N D:ASP407 3.7 26.0 1.0
CB D:ASP407 3.7 29.2 1.0
CA D:THR406 3.8 23.3 1.0
O D:LEU405 4.0 23.3 1.0
N D:THR406 4.0 22.8 1.0
CD2 D:LEU405 4.0 24.3 1.0
C D:LEU405 4.0 24.9 1.0
C2 D:4OQ601 4.1 25.6 1.0
CD1 D:LEU380 4.2 18.2 1.0
CA D:ASP407 4.2 27.0 1.0
CE1 D:HIS387 4.4 24.7 1.0
CB D:LEU405 4.4 20.0 1.0
CG D:HIS387 4.4 24.1 1.0
CD1 D:LEU405 4.4 23.2 1.0
N1 D:4OQ601 4.7 26.1 1.0
CG2 D:ILE327 4.8 20.7 1.0
CA D:LEU405 4.9 20.1 1.0
CG D:ASP407 4.9 36.4 1.0
O D:HOH851 4.9 31.3 1.0

Reference:

A.S.Karpov, P.Amiri, C.Bellamacina, M.H.Bellance, W.Breitenstein, D.Daniel, R.Denay, D.Fabbro, C.Fernandez, I.Galuba, S.Guerro-Lagasse, S.Gutmann, L.Hinh, W.Jahnke, J.Klopp, A.Lai, M.K.Lindvall, S.Ma, H.Mobitz, S.Pecchi, G.Rummel, K.Shoemaker, J.Trappe, C.Voliva, S.W.Cowan-Jacob, A.L.Marzinzik. Optimization of A Dibenzodiazepine Hit to A Potent and Selective Allosteric PAK1 Inhibitor. Acs Med.Chem.Lett. V. 6 776 2015.
ISSN: ISSN 1948-5875
PubMed: 26191365
DOI: 10.1021/ACSMEDCHEMLETT.5B00102
Page generated: Tue Jul 15 01:57:27 2025

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