Atomistry » Fluorine » PDB 4zga-4zzi » 4zjj
Atomistry »
  Fluorine »
    PDB 4zga-4zzi »
      4zjj »

Fluorine in PDB 4zjj: PAK1 in Complex with (S)-N-(Tert-Butyl)-3-((2-Chloro-5-Ethyl-8-Fluoro- Dibenzodiazepin-11-Yl)Amino)Pyrrolidine-1-Carboxamide

Enzymatic activity of PAK1 in Complex with (S)-N-(Tert-Butyl)-3-((2-Chloro-5-Ethyl-8-Fluoro- Dibenzodiazepin-11-Yl)Amino)Pyrrolidine-1-Carboxamide

All present enzymatic activity of PAK1 in Complex with (S)-N-(Tert-Butyl)-3-((2-Chloro-5-Ethyl-8-Fluoro- Dibenzodiazepin-11-Yl)Amino)Pyrrolidine-1-Carboxamide:
2.7.11.1;

Protein crystallography data

The structure of PAK1 in Complex with (S)-N-(Tert-Butyl)-3-((2-Chloro-5-Ethyl-8-Fluoro- Dibenzodiazepin-11-Yl)Amino)Pyrrolidine-1-Carboxamide, PDB code: 4zjj 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) 116.36 / 2.20
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 110.330, 113.790, 116.360, 90.00, 90.00, 90.00
R / Rfree (%) 20.1 / 23.8

Other elements in 4zjj:

The structure of PAK1 in Complex with (S)-N-(Tert-Butyl)-3-((2-Chloro-5-Ethyl-8-Fluoro- Dibenzodiazepin-11-Yl)Amino)Pyrrolidine-1-Carboxamide 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 (S)-N-(Tert-Butyl)-3-((2-Chloro-5-Ethyl-8-Fluoro- Dibenzodiazepin-11-Yl)Amino)Pyrrolidine-1-Carboxamide (pdb code 4zjj). 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 (S)-N-(Tert-Butyl)-3-((2-Chloro-5-Ethyl-8-Fluoro- Dibenzodiazepin-11-Yl)Amino)Pyrrolidine-1-Carboxamide, PDB code: 4zjj:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 4zjj

Go back to Fluorine Binding Sites List in 4zjj
Fluorine binding site 1 out of 4 in the PAK1 in Complex with (S)-N-(Tert-Butyl)-3-((2-Chloro-5-Ethyl-8-Fluoro- Dibenzodiazepin-11-Yl)Amino)Pyrrolidine-1-Carboxamide


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 (S)-N-(Tert-Butyl)-3-((2-Chloro-5-Ethyl-8-Fluoro- Dibenzodiazepin-11-Yl)Amino)Pyrrolidine-1-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:21.3
occ:1.00
 F A:4OR601 0.0 21.3 1.0
C5 A:4OR601 1.4 21.7 1.0
C6 A:4OR601 2.3 19.5 1.0
C4 A:4OR601 2.4 18.2 1.0
NE2 A:HIS387 3.1 18.4 1.0
CD2 A:HIS387 3.1 18.1 1.0
C A:THR406 3.3 16.1 1.0
O A:THR406 3.3 13.1 1.0
CG A:LEU405 3.5 16.0 1.0
C3 A:4OR601 3.6 15.4 1.0
C7 A:4OR601 3.6 20.8 1.0
N A:ASP407 3.7 16.5 1.0
CA A:THR406 3.7 13.1 1.0
O A:LEU405 3.7 13.7 1.0
CB A:ASP407 3.7 18.2 1.0
C A:LEU405 3.9 16.5 1.0
N A:THR406 3.9 12.5 1.0
CD2 A:LEU405 4.1 17.3 1.0
C2 A:4OR601 4.1 18.7 1.0
CD1 A:LEU380 4.2 19.2 1.0
CA A:ASP407 4.2 16.6 1.0
CB A:LEU405 4.3 14.7 1.0
CD1 A:LEU405 4.4 13.8 1.0
CE1 A:HIS387 4.4 17.5 1.0
CG A:HIS387 4.5 16.2 1.0
O A:HOH791 4.7 22.4 1.0
N1 A:4OR601 4.7 23.6 1.0
CA A:LEU405 4.7 14.9 1.0
CG2 A:ILE327 4.9 15.1 1.0
O A:HOH705 4.9 23.6 1.0
CG A:ASP407 5.0 20.3 1.0

Fluorine binding site 2 out of 4 in 4zjj

Go back to Fluorine Binding Sites List in 4zjj
Fluorine binding site 2 out of 4 in the PAK1 in Complex with (S)-N-(Tert-Butyl)-3-((2-Chloro-5-Ethyl-8-Fluoro- Dibenzodiazepin-11-Yl)Amino)Pyrrolidine-1-Carboxamide


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 (S)-N-(Tert-Butyl)-3-((2-Chloro-5-Ethyl-8-Fluoro- Dibenzodiazepin-11-Yl)Amino)Pyrrolidine-1-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F601

b:28.8
occ:1.00
 F B:4OR601 0.0 28.8 1.0
C5 B:4OR601 1.4 34.2 1.0
C4 B:4OR601 2.3 33.4 1.0
C6 B:4OR601 2.4 36.6 1.0
CD2 B:HIS387 3.2 27.8 1.0
NE2 B:HIS387 3.2 27.3 1.0
C B:THR406 3.4 26.2 1.0
O B:THR406 3.5 26.3 1.0
CG B:LEU405 3.6 28.7 1.0
C3 B:4OR601 3.6 35.3 1.0
C7 B:4OR601 3.6 37.8 1.0
CB B:ASP407 3.8 24.8 1.0
O B:LEU405 3.8 25.7 1.0
N B:ASP407 3.8 23.1 1.0
CA B:THR406 3.9 22.4 1.0
C B:LEU405 3.9 25.4 1.0
N B:THR406 4.0 21.7 1.0
CD2 B:LEU405 4.1 28.3 1.0
CD1 B:LEU380 4.1 27.1 1.0
C2 B:4OR601 4.1 36.6 1.0
CA B:ASP407 4.3 22.5 1.0
CB B:LEU405 4.4 23.9 1.0
CD1 B:LEU405 4.5 29.2 1.0
CG B:HIS387 4.5 26.4 1.0
CE1 B:HIS387 4.6 26.4 1.0
N1 B:4OR601 4.7 35.1 1.0
O B:HOH760 4.8 34.9 1.0
CA B:LEU405 4.8 23.8 1.0
CG2 B:ILE327 4.8 29.4 1.0
CG B:ASP407 4.9 34.7 1.0

Fluorine binding site 3 out of 4 in 4zjj

Go back to Fluorine Binding Sites List in 4zjj
Fluorine binding site 3 out of 4 in the PAK1 in Complex with (S)-N-(Tert-Butyl)-3-((2-Chloro-5-Ethyl-8-Fluoro- Dibenzodiazepin-11-Yl)Amino)Pyrrolidine-1-Carboxamide


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 (S)-N-(Tert-Butyl)-3-((2-Chloro-5-Ethyl-8-Fluoro- Dibenzodiazepin-11-Yl)Amino)Pyrrolidine-1-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F601

b:34.7
occ:1.00
 F C:4OR601 0.0 34.7 1.0
C5 C:4OR601 1.4 33.2 1.0
C6 C:4OR601 2.3 30.3 1.0
C4 C:4OR601 2.3 34.3 1.0
NE2 C:HIS387 3.1 26.4 1.0
CD2 C:HIS387 3.2 26.9 1.0
C C:THR406 3.3 33.2 1.0
O C:THR406 3.3 31.4 1.0
CG C:LEU405 3.4 30.8 1.0
O C:LEU405 3.6 25.6 1.0
C3 C:4OR601 3.6 33.1 1.0
C7 C:4OR601 3.6 32.2 1.0
C C:LEU405 3.7 26.6 1.0
CA C:THR406 3.7 26.1 1.0
N C:ASP407 3.7 32.6 1.0
N C:THR406 3.8 23.8 1.0
CB C:ASP407 3.8 36.5 1.0
CD2 C:LEU405 3.9 29.4 1.0
C2 C:4OR601 4.1 30.2 1.0
CB C:LEU405 4.1 25.3 1.0
CD1 C:LEU405 4.2 31.7 1.0
CD1 C:LEU380 4.2 25.1 1.0
CA C:ASP407 4.3 34.3 1.0
CE1 C:HIS387 4.5 25.7 1.0
CG C:HIS387 4.5 26.1 1.0
CA C:LEU405 4.5 24.5 1.0
CG2 C:ILE327 4.7 25.2 1.0
N1 C:4OR601 4.7 31.6 1.0
O C:HOH812 4.8 32.2 1.0
CG C:ASP407 4.9 47.0 1.0

Fluorine binding site 4 out of 4 in 4zjj

Go back to Fluorine Binding Sites List in 4zjj
Fluorine binding site 4 out of 4 in the PAK1 in Complex with (S)-N-(Tert-Butyl)-3-((2-Chloro-5-Ethyl-8-Fluoro- Dibenzodiazepin-11-Yl)Amino)Pyrrolidine-1-Carboxamide


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 (S)-N-(Tert-Butyl)-3-((2-Chloro-5-Ethyl-8-Fluoro- Dibenzodiazepin-11-Yl)Amino)Pyrrolidine-1-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F601

b:21.8
occ:1.00
 F D:4OR601 0.0 21.8 1.0
C5 D:4OR601 1.4 22.3 1.0
C6 D:4OR601 2.3 21.6 1.0
C4 D:4OR601 2.3 21.9 1.0
CD2 D:HIS387 3.2 20.5 1.0
CG D:LEU405 3.2 24.0 1.0
NE2 D:HIS387 3.2 20.7 1.0
O D:THR406 3.3 28.8 1.0
C D:THR406 3.3 30.2 1.0
C3 D:4OR601 3.6 23.4 1.0
O D:LEU405 3.6 26.3 1.0
C D:LEU405 3.6 26.4 1.0
C7 D:4OR601 3.6 23.0 1.0
N D:THR406 3.6 24.4 1.0
CA D:THR406 3.7 24.4 1.0
N D:ASP407 3.7 29.3 1.0
CB D:ASP407 3.8 31.8 1.0
CD2 D:LEU405 3.8 22.9 1.0
CB D:LEU405 4.0 20.3 1.0
CD1 D:LEU380 4.1 17.8 1.0
C2 D:4OR601 4.1 23.1 1.0
CD1 D:LEU405 4.1 24.9 1.0
CA D:ASP407 4.3 29.9 1.0
CA D:LEU405 4.4 20.0 1.0
CE1 D:HIS387 4.5 20.2 1.0
CG2 D:ILE327 4.5 17.7 1.0
CG D:HIS387 4.6 19.9 1.0
N1 D:4OR601 4.7 23.6 1.0
CB D:ILE327 4.9 18.8 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 01:57:32 2025

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy