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Magnesium 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
Chlorine (Cl) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium 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 Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4zjj

Go back to Magnesium Binding Sites List in 4zjj
Magnesium binding site 1 out of 2 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 Magnesium with other atoms in the Mg 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
C:Mg602

b:36.3
occ:1.00
 O C:GLU461 2.1 22.1 1.0
O C:HOH704 2.2 29.9 1.0
O C:HOH826 2.3 38.0 1.0
O C:HOH795 2.3 33.1 1.0
C C:GLU461 3.3 25.5 1.0
C C:PRO462 3.9 27.1 1.0
O C:PRO462 4.1 23.2 1.0
CA C:PRO462 4.1 24.9 1.0
O C:GLU456 4.1 23.4 1.0
N C:PRO462 4.2 24.5 1.0
CA C:GLU461 4.2 22.9 1.0
N C:GLU461 4.3 25.6 1.0
N C:PRO463 4.4 26.6 1.0
O C:ILE458 4.4 23.7 1.0
CB C:GLU461 4.5 23.0 1.0
CA C:GLU456 4.6 23.4 1.0
O C:ILE455 4.7 25.1 1.0
C C:GLU456 4.7 23.6 1.0
CD C:PRO463 5.0 29.4 1.0

Magnesium binding site 2 out of 2 in 4zjj

Go back to Magnesium Binding Sites List in 4zjj
Magnesium binding site 2 out of 2 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 Magnesium with other atoms in the Mg 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
D:Mg602

b:42.1
occ:1.00
 O D:HOH709 1.9 29.6 1.0
O D:GLU461 2.2 29.6 1.0
O D:HOH701 2.2 29.3 1.0
O D:HOH747 2.5 39.4 1.0
C D:GLU461 3.4 31.9 1.0
O D:GLU456 3.9 26.5 1.0
C D:PRO462 3.9 34.9 1.0
O D:PRO462 4.1 34.2 1.0
CA D:PRO462 4.1 31.9 1.0
N D:PRO462 4.2 31.5 1.0
OE1 D:GLU456 4.2 65.6 1.0
O D:ILE458 4.3 28.5 1.0
N D:PRO463 4.3 29.8 1.0
CA D:GLU461 4.4 29.0 1.0
CA D:GLU456 4.4 25.8 1.0
N D:GLU461 4.5 31.6 1.0
C D:GLU456 4.5 27.5 1.0
O D:ILE455 4.5 26.9 1.0
CB D:GLU461 4.5 28.5 1.0
CD D:PRO463 4.9 31.3 1.0
CA D:PRO463 5.0 27.4 1.0
CD D:GLU456 5.0 79.9 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: Sun Sep 29 00:03:37 2024

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