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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: Thu Aug 1 07:18:20 2024

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