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Chlorine 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:

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

Chlorine Binding Sites:

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

Chlorine binding site 1 out of 4 in 4zji

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Chlorine 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 Chlorine with other atoms in the Cl 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:Cl601

b:23.7
occ:1.00
 CL A:4OQ601 0.0 23.7 1.0
C11 A:4OQ601 1.7 19.8 1.0
C10 A:4OQ601 2.7 16.9 1.0
C12 A:4OQ601 2.7 18.4 1.0
CB A:ASN383 3.5 20.1 1.0
CG A:ASN383 3.6 29.6 1.0
ND2 A:ASN383 3.7 19.4 1.0
CE2 A:PHE379 3.8 25.3 1.0
CG2 A:VAL318 3.8 29.5 1.0
CZ A:PHE379 3.8 23.1 1.0
CB A:ASN322 3.9 18.7 1.0
O A:VAL318 4.0 23.9 1.0
C13 A:4OQ601 4.0 18.8 1.0
C9 A:4OQ601 4.0 17.6 1.0
OD1 A:ASN383 4.3 21.6 1.0
CG1 A:VAL318 4.4 28.5 1.0
C A:VAL318 4.4 26.5 1.0
CD2 A:LEU380 4.5 17.4 1.0
CG A:ASN322 4.5 29.9 1.0
C14 A:4OQ601 4.5 18.0 1.0
CG2 A:VAL385 4.6 20.5 1.0
CB A:VAL318 4.6 29.3 1.0
ND2 A:ASN322 4.6 21.0 1.0
O A:ASN322 4.7 22.4 1.0
CE1 A:PHE379 4.7 24.6 1.0
CD2 A:PHE379 4.7 22.6 1.0
CA A:MET319 4.9 20.9 1.0
N A:MET319 4.9 22.4 1.0

Chlorine binding site 2 out of 4 in 4zji

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Chlorine 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 Chlorine with other atoms in the Cl 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:Cl601

b:33.3
occ:1.00
 CL B:4OQ601 0.0 33.3 1.0
C11 B:4OQ601 1.7 27.3 1.0
C10 B:4OQ601 2.7 26.7 1.0
C12 B:4OQ601 2.7 27.4 1.0
CG1 B:VAL318 3.5 44.2 1.0
CB B:ASN383 3.6 31.4 1.0
CG B:ASN383 3.6 39.6 1.0
ND2 B:ASN383 3.7 26.2 1.0
CZ B:PHE379 3.7 32.1 1.0
CE2 B:PHE379 3.7 33.8 1.0
CB B:ASN322 3.9 33.0 1.0
O B:VAL318 4.0 39.5 1.0
C13 B:4OQ601 4.0 27.4 1.0
C9 B:4OQ601 4.0 27.3 1.0
OD1 B:ASN383 4.3 33.1 1.0
C B:VAL318 4.5 40.7 1.0
CD2 B:LEU380 4.5 24.9 1.0
CG B:ASN322 4.5 50.9 1.0
C14 B:4OQ601 4.5 28.6 1.0
OD1 B:ASN322 4.5 43.2 1.0
CG2 B:VAL385 4.6 28.3 1.0
CE1 B:PHE379 4.7 34.3 1.0
O B:ASN322 4.7 33.1 1.0
CD2 B:PHE379 4.7 31.5 1.0
CB B:VAL318 4.8 45.0 1.0

Chlorine binding site 3 out of 4 in 4zji

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Chlorine 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 Chlorine with other atoms in the Cl 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:Cl601

b:30.4
occ:1.00
 CL C:4OQ601 0.0 30.4 1.0
C11 C:4OQ601 1.7 26.4 1.0
C10 C:4OQ601 2.7 25.0 1.0
C12 C:4OQ601 2.7 26.5 1.0
CG C:ASN383 3.5 43.2 1.0
CB C:ASN383 3.6 29.9 1.0
CG1 C:VAL318 3.6 34.1 1.0
ND2 C:ASN383 3.7 28.8 1.0
CB C:ASN322 3.7 30.0 1.0
CZ C:PHE379 3.8 28.1 1.0
CE2 C:PHE379 3.8 29.1 1.0
C13 C:4OQ601 4.0 24.8 1.0
C9 C:4OQ601 4.0 27.6 1.0
OD1 C:ASN383 4.1 37.9 1.0
CG C:ASN322 4.3 44.7 1.0
O C:VAL318 4.3 36.5 1.0
ND2 C:ASN322 4.3 30.6 1.0
C14 C:4OQ601 4.5 25.8 1.0
CD2 C:LEU380 4.6 26.6 1.0
CE1 C:PHE379 4.7 29.2 1.0
CG2 C:VAL385 4.7 31.4 1.0
O C:ASN322 4.8 30.9 1.0
C C:VAL318 4.8 36.1 1.0
CD2 C:PHE379 4.8 27.1 1.0
CA C:ASN322 5.0 31.0 1.0

Chlorine binding site 4 out of 4 in 4zji

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Chlorine 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 Chlorine with other atoms in the Cl 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:Cl601

b:25.2
occ:1.00
 CL D:4OQ601 0.0 25.2 1.0
C11 D:4OQ601 1.7 20.0 1.0
C10 D:4OQ601 2.7 19.7 1.0
C12 D:4OQ601 2.7 20.8 1.0
CG D:ASN383 3.5 30.4 1.0
CB D:ASN383 3.5 20.7 1.0
CG1 D:VAL318 3.6 24.0 1.0
ND2 D:ASN383 3.6 21.4 1.0
CB D:ASN322 3.7 17.4 1.0
CZ D:PHE379 3.8 21.9 1.0
CE2 D:PHE379 3.9 23.7 1.0
C13 D:4OQ601 4.0 20.1 1.0
C9 D:4OQ601 4.0 20.8 1.0
OD1 D:ASN383 4.1 29.8 1.0
CG D:ASN322 4.2 30.7 1.0
ND2 D:ASN322 4.4 22.2 1.0
O D:VAL318 4.4 24.6 1.0
C14 D:4OQ601 4.5 22.0 1.0
CD2 D:LEU380 4.6 20.3 1.0
CG2 D:VAL385 4.7 24.9 1.0
CE1 D:PHE379 4.7 24.0 1.0
O D:ASN322 4.7 21.9 1.0
CD2 D:PHE379 4.8 21.4 1.0
C D:VAL318 4.9 25.6 1.0
O D:HOH722 4.9 37.1 1.0
CA D:ASN322 5.0 21.5 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 11 23:48:00 2025

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