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Chlorine 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:

Fluorine (F) 4 atoms
Magnesium (Mg) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 4 binding sites of Chlorine 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 Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 4zjj

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Chlorine 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 Chlorine with other atoms in the Cl 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:Cl601

b:19.8
occ:1.00
 CL A:4OR601 0.0 19.8 1.0
C20 A:4OR601 1.7 19.9 1.0
C19 A:4OR601 2.7 19.3 1.0
C21 A:4OR601 2.7 18.4 1.0
CG1 A:VAL318 3.5 24.6 1.0
CB A:ASN383 3.6 17.4 1.0
CG A:ASN383 3.7 23.2 1.0
ND2 A:ASN383 3.8 11.4 1.0
CZ A:PHE379 3.9 19.2 1.0
CE2 A:PHE379 3.9 19.6 1.0
CB A:ASN322 3.9 22.4 1.0
C22 A:4OR601 4.0 19.4 1.0
C18 A:4OR601 4.0 20.5 1.0
O A:VAL318 4.2 27.3 1.0
OD1 A:ASN383 4.3 17.8 1.0
C A:VAL318 4.5 28.1 1.0
C23 A:4OR601 4.5 19.0 1.0
CD2 A:LEU380 4.6 20.1 1.0
O A:ASN322 4.6 23.2 1.0
CG2 A:VAL385 4.6 19.2 1.0
CG A:ASN322 4.7 32.4 1.0
CA A:MET319 4.7 22.2 1.0
O A:HOH817 4.8 23.2 1.0
N A:MET319 4.8 23.8 1.0
CE1 A:PHE379 4.8 20.8 1.0
OD1 A:ASN322 4.9 22.2 1.0
CB A:VAL318 4.9 25.4 1.0
CD2 A:PHE379 4.9 17.2 1.0

Chlorine binding site 2 out of 4 in 4zjj

Go back to Chlorine Binding Sites List in 4zjj
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl601

b:36.5
occ:1.00
 CL B:4OR601 0.0 36.5 1.0
C20 B:4OR601 1.7 34.6 1.0
C19 B:4OR601 2.7 33.1 1.0
C21 B:4OR601 2.7 33.4 1.0
CB B:ASN383 3.5 35.5 1.0
CG B:ASN383 3.5 50.0 1.0
ND2 B:ASN383 3.6 37.2 1.0
CZ B:PHE379 3.8 41.0 1.0
CE2 B:PHE379 3.8 41.4 1.0
C22 B:4OR601 4.0 31.4 1.0
C18 B:4OR601 4.0 31.3 1.0
CB B:ASN322 4.0 35.7 1.0
OD1 B:ASN383 4.1 44.0 1.0
O B:VAL318 4.4 43.2 1.0
C23 B:4OR601 4.5 29.9 1.0
CD2 B:LEU380 4.5 28.6 1.0
O B:ASN322 4.7 36.3 1.0
CE1 B:PHE379 4.7 43.0 1.0
CG2 B:VAL385 4.7 28.5 1.0
C B:VAL318 4.7 43.3 1.0
CD2 B:PHE379 4.7 38.3 1.0
CG B:ASN322 4.7 53.4 1.0
CA B:MET319 4.9 37.7 1.0
OD1 B:ASN322 4.9 46.2 1.0
N B:MET319 5.0 38.4 1.0
CA B:ASN383 5.0 32.7 1.0

Chlorine binding site 3 out of 4 in 4zjj

Go back to Chlorine Binding Sites List in 4zjj
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl601

b:33.9
occ:1.00
 CL C:4OR601 0.0 33.9 1.0
C20 C:4OR601 1.7 30.2 1.0
C19 C:4OR601 2.7 30.4 1.0
C21 C:4OR601 2.7 28.2 1.0
CB C:ASN383 3.5 31.8 1.0
CG C:ASN383 3.5 43.4 1.0
ND2 C:ASN383 3.6 30.3 1.0
CG1 C:VAL318 3.6 37.0 1.0
CZ C:PHE379 3.7 30.9 1.0
CE2 C:PHE379 3.8 31.7 1.0
CB C:ASN322 3.9 32.5 1.0
C22 C:4OR601 4.0 25.9 1.0
C18 C:4OR601 4.0 29.6 1.0
OD1 C:ASN383 4.1 40.9 1.0
O C:VAL318 4.3 37.8 1.0
C23 C:4OR601 4.5 27.4 1.0
CD2 C:LEU380 4.5 25.6 1.0
O C:ASN322 4.6 35.4 1.0
CG C:ASN322 4.6 46.5 1.0
C C:VAL318 4.6 37.9 1.0
CE1 C:PHE379 4.7 32.1 1.0
CD2 C:PHE379 4.7 28.8 1.0
CG2 C:VAL385 4.7 31.7 1.0
OD1 C:ASN322 4.8 39.9 1.0
O C:HOH810 4.8 32.8 1.0
CA C:MET319 4.8 29.7 1.0
N C:MET319 4.9 31.5 1.0
CB C:VAL318 5.0 38.7 1.0

Chlorine binding site 4 out of 4 in 4zjj

Go back to Chlorine Binding Sites List in 4zjj
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl601

b:28.4
occ:1.00
 CL D:4OR601 0.0 28.4 1.0
C20 D:4OR601 1.7 22.8 1.0
C21 D:4OR601 2.7 20.2 1.0
C19 D:4OR601 2.7 20.6 1.0
CB D:ASN383 3.6 19.1 1.0
CG1 D:VAL318 3.6 24.9 1.0
CG D:ASN383 3.6 26.7 1.0
ND2 D:ASN383 3.7 24.0 1.0
CB D:ASN322 3.8 17.3 1.0
CZ D:PHE379 3.9 18.3 1.0
CE2 D:PHE379 3.9 19.3 1.0
C22 D:4OR601 4.0 20.7 1.0
C18 D:4OR601 4.0 20.8 1.0
OD1 D:ASN383 4.2 27.9 1.0
O D:VAL318 4.2 26.5 1.0
O D:ASN322 4.5 19.7 1.0
C23 D:4OR601 4.5 20.8 1.0
CG D:ASN322 4.5 31.8 1.0
C D:VAL318 4.6 25.1 1.0
CD2 D:LEU380 4.6 20.9 1.0
OD1 D:ASN322 4.7 29.8 1.0
CG2 D:VAL385 4.7 25.3 1.0
CA D:MET319 4.8 17.6 1.0
CE1 D:PHE379 4.8 18.7 1.0
N D:MET319 4.9 19.1 1.0
CD2 D:PHE379 4.9 17.1 1.0
O D:HOH803 4.9 24.4 1.0
CB D:VAL318 5.0 25.4 1.0
CA D:ASN322 5.0 18.9 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: Fri Jul 26 04:40:56 2024

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