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Chlorine in PDB 4ixu: Crystal Structure of Human Arginase-2 Complexed with Inhibitor 11D: {(5R)-5-Amino-5-Carboxy-5-[(3-Endo)-8-(3,4-Dichlorobenzyl)-8- Azabicyclo[3.2.1]Oct-3-Yl]Pentyl}(Trihydroxy)Borate(1-)

Enzymatic activity of Crystal Structure of Human Arginase-2 Complexed with Inhibitor 11D: {(5R)-5-Amino-5-Carboxy-5-[(3-Endo)-8-(3,4-Dichlorobenzyl)-8- Azabicyclo[3.2.1]Oct-3-Yl]Pentyl}(Trihydroxy)Borate(1-)

All present enzymatic activity of Crystal Structure of Human Arginase-2 Complexed with Inhibitor 11D: {(5R)-5-Amino-5-Carboxy-5-[(3-Endo)-8-(3,4-Dichlorobenzyl)-8- Azabicyclo[3.2.1]Oct-3-Yl]Pentyl}(Trihydroxy)Borate(1-):
3.5.3.1;

Protein crystallography data

The structure of Crystal Structure of Human Arginase-2 Complexed with Inhibitor 11D: {(5R)-5-Amino-5-Carboxy-5-[(3-Endo)-8-(3,4-Dichlorobenzyl)-8- Azabicyclo[3.2.1]Oct-3-Yl]Pentyl}(Trihydroxy)Borate(1-), PDB code: 4ixu was solved by A.Cousido-Siah, A.Mitschler, F.X.Ruiz, D.Whitehouse, P.Beckett, M.C.Vanzandt, M.K.Ji, T.Ryder, R.Jagdmann, M.Andreoli, J.Olczak, M.Mazur, W.Czestkowski, W.Piotrowska, H.Schroeter, A.Golebiowski, A.Podjarny, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.34 / 1.90
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 127.400, 127.400, 159.249, 90.00, 90.00, 90.00
R / Rfree (%) 16.7 / 19.3

Other elements in 4ixu:

The structure of Crystal Structure of Human Arginase-2 Complexed with Inhibitor 11D: {(5R)-5-Amino-5-Carboxy-5-[(3-Endo)-8-(3,4-Dichlorobenzyl)-8- Azabicyclo[3.2.1]Oct-3-Yl]Pentyl}(Trihydroxy)Borate(1-) also contains other interesting chemical elements:

Manganese (Mn) 6 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Human Arginase-2 Complexed with Inhibitor 11D: {(5R)-5-Amino-5-Carboxy-5-[(3-Endo)-8-(3,4-Dichlorobenzyl)-8- Azabicyclo[3.2.1]Oct-3-Yl]Pentyl}(Trihydroxy)Borate(1-) (pdb code 4ixu). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Crystal Structure of Human Arginase-2 Complexed with Inhibitor 11D: {(5R)-5-Amino-5-Carboxy-5-[(3-Endo)-8-(3,4-Dichlorobenzyl)-8- Azabicyclo[3.2.1]Oct-3-Yl]Pentyl}(Trihydroxy)Borate(1-), PDB code: 4ixu:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 4ixu

Go back to Chlorine Binding Sites List in 4ixu
Chlorine binding site 1 out of 6 in the Crystal Structure of Human Arginase-2 Complexed with Inhibitor 11D: {(5R)-5-Amino-5-Carboxy-5-[(3-Endo)-8-(3,4-Dichlorobenzyl)-8- Azabicyclo[3.2.1]Oct-3-Yl]Pentyl}(Trihydroxy)Borate(1-)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Human Arginase-2 Complexed with Inhibitor 11D: {(5R)-5-Amino-5-Carboxy-5-[(3-Endo)-8-(3,4-Dichlorobenzyl)-8- Azabicyclo[3.2.1]Oct-3-Yl]Pentyl}(Trihydroxy)Borate(1-) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:82.8
occ:1.00
 CL2 A:38I406 0.0 82.8 1.0
C26 A:38I406 1.8 84.1 1.0
O A:HOH659 2.3 30.6 1.0
C27 A:38I406 2.7 69.8 1.0
C25 A:38I406 2.8 0.3 1.0
CL1 A:38I406 3.3 0.1 1.0
OG A:SER155 3.7 16.1 1.0
C22 A:38I406 4.0 65.8 1.0
CB A:SER155 4.0 13.6 1.0
C24 A:38I406 4.1 0.8 1.0
O A:HOH672 4.3 27.1 1.0
CD A:PRO203 4.3 19.1 1.0
OD1 A:ASP202 4.5 22.5 1.0
C23 A:38I406 4.6 84.8 1.0
CG A:ASP202 4.6 22.8 1.0
CB A:ASP202 4.7 15.7 1.0

Chlorine binding site 2 out of 6 in 4ixu

Go back to Chlorine Binding Sites List in 4ixu
Chlorine binding site 2 out of 6 in the Crystal Structure of Human Arginase-2 Complexed with Inhibitor 11D: {(5R)-5-Amino-5-Carboxy-5-[(3-Endo)-8-(3,4-Dichlorobenzyl)-8- Azabicyclo[3.2.1]Oct-3-Yl]Pentyl}(Trihydroxy)Borate(1-)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Human Arginase-2 Complexed with Inhibitor 11D: {(5R)-5-Amino-5-Carboxy-5-[(3-Endo)-8-(3,4-Dichlorobenzyl)-8- Azabicyclo[3.2.1]Oct-3-Yl]Pentyl}(Trihydroxy)Borate(1-) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:0.1
occ:1.00
 CL1 A:38I406 0.0 0.1 1.0
C25 A:38I406 1.8 0.3 1.0
C24 A:38I406 2.7 0.8 1.0
C26 A:38I406 2.8 84.1 1.0
CL2 A:38I406 3.3 82.8 1.0
C23 A:38I406 4.0 84.8 1.0
C27 A:38I406 4.1 69.8 1.0
C22 A:38I406 4.5 65.8 1.0

Chlorine binding site 3 out of 6 in 4ixu

Go back to Chlorine Binding Sites List in 4ixu
Chlorine binding site 3 out of 6 in the Crystal Structure of Human Arginase-2 Complexed with Inhibitor 11D: {(5R)-5-Amino-5-Carboxy-5-[(3-Endo)-8-(3,4-Dichlorobenzyl)-8- Azabicyclo[3.2.1]Oct-3-Yl]Pentyl}(Trihydroxy)Borate(1-)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Human Arginase-2 Complexed with Inhibitor 11D: {(5R)-5-Amino-5-Carboxy-5-[(3-Endo)-8-(3,4-Dichlorobenzyl)-8- Azabicyclo[3.2.1]Oct-3-Yl]Pentyl}(Trihydroxy)Borate(1-) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl406

b:70.5
occ:1.00
 CL2 B:38I406 0.0 70.5 1.0
C26 B:38I406 1.8 70.5 1.0
C27 B:38I406 2.7 60.5 1.0
C25 B:38I406 2.9 85.5 1.0
OG B:SER155 3.4 17.3 1.0
CL1 B:38I406 3.5 1.0 1.0
CB B:SER155 3.7 13.4 1.0
O B:HOH515 3.8 26.8 1.0
C22 B:38I406 4.0 59.6 1.0
C24 B:38I406 4.1 86.0 1.0
CD B:PRO203 4.3 18.1 1.0
CG B:ASP202 4.3 24.2 1.0
CB B:ASP202 4.4 15.0 1.0
OD1 B:ASP202 4.4 26.2 1.0
O B:HOH689 4.5 42.6 0.3
C23 B:38I406 4.6 68.8 1.0
OD2 B:ASP202 4.7 17.7 1.0
O B:HOH532 4.8 25.2 1.0

Chlorine binding site 4 out of 6 in 4ixu

Go back to Chlorine Binding Sites List in 4ixu
Chlorine binding site 4 out of 6 in the Crystal Structure of Human Arginase-2 Complexed with Inhibitor 11D: {(5R)-5-Amino-5-Carboxy-5-[(3-Endo)-8-(3,4-Dichlorobenzyl)-8- Azabicyclo[3.2.1]Oct-3-Yl]Pentyl}(Trihydroxy)Borate(1-)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Human Arginase-2 Complexed with Inhibitor 11D: {(5R)-5-Amino-5-Carboxy-5-[(3-Endo)-8-(3,4-Dichlorobenzyl)-8- Azabicyclo[3.2.1]Oct-3-Yl]Pentyl}(Trihydroxy)Borate(1-) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl406

b:1.0
occ:1.00
 CL1 B:38I406 0.0 1.0 1.0
C25 B:38I406 1.8 85.5 1.0
C24 B:38I406 2.6 86.0 1.0
O B:HOH689 2.7 42.6 0.3
C26 B:38I406 2.8 70.5 1.0
CL2 B:38I406 3.5 70.5 1.0
C23 B:38I406 4.0 68.8 1.0
C27 B:38I406 4.1 60.5 1.0
C22 B:38I406 4.5 59.6 1.0
O B:HOH689 4.6 42.6 0.7
OG B:SER155 4.7 17.3 1.0
CB B:SER155 4.9 13.4 1.0

Chlorine binding site 5 out of 6 in 4ixu

Go back to Chlorine Binding Sites List in 4ixu
Chlorine binding site 5 out of 6 in the Crystal Structure of Human Arginase-2 Complexed with Inhibitor 11D: {(5R)-5-Amino-5-Carboxy-5-[(3-Endo)-8-(3,4-Dichlorobenzyl)-8- Azabicyclo[3.2.1]Oct-3-Yl]Pentyl}(Trihydroxy)Borate(1-)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Human Arginase-2 Complexed with Inhibitor 11D: {(5R)-5-Amino-5-Carboxy-5-[(3-Endo)-8-(3,4-Dichlorobenzyl)-8- Azabicyclo[3.2.1]Oct-3-Yl]Pentyl}(Trihydroxy)Borate(1-) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl406

b:86.4
occ:1.00
 CL2 C:38I406 0.0 86.4 1.0
C26 C:38I406 1.8 82.0 1.0
C27 C:38I406 2.8 69.9 1.0
C25 C:38I406 2.8 0.1 1.0
CL1 C:38I406 3.3 0.5 1.0
O C:HOH637 3.6 28.0 1.0
OG C:SER155 3.9 17.3 1.0
CD C:PRO203 3.9 22.8 1.0
C22 C:38I406 4.1 69.6 1.0
C24 C:38I406 4.1 97.8 1.0
CB C:SER155 4.1 20.8 1.0
CB C:ASP202 4.2 13.8 1.0
CG C:ASP202 4.3 25.2 1.0
CD C:PRO204 4.5 16.8 1.0
C23 C:38I406 4.6 85.3 1.0
OD1 C:ASP202 4.6 24.4 1.0
OD2 C:ASP202 4.7 20.3 1.0
CG C:PRO203 4.8 27.4 1.0
N C:PRO203 4.9 20.1 1.0
CA C:ASP202 4.9 17.0 1.0

Chlorine binding site 6 out of 6 in 4ixu

Go back to Chlorine Binding Sites List in 4ixu
Chlorine binding site 6 out of 6 in the Crystal Structure of Human Arginase-2 Complexed with Inhibitor 11D: {(5R)-5-Amino-5-Carboxy-5-[(3-Endo)-8-(3,4-Dichlorobenzyl)-8- Azabicyclo[3.2.1]Oct-3-Yl]Pentyl}(Trihydroxy)Borate(1-)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Human Arginase-2 Complexed with Inhibitor 11D: {(5R)-5-Amino-5-Carboxy-5-[(3-Endo)-8-(3,4-Dichlorobenzyl)-8- Azabicyclo[3.2.1]Oct-3-Yl]Pentyl}(Trihydroxy)Borate(1-) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl406

b:0.5
occ:1.00
 CL1 C:38I406 0.0 0.5 1.0
C25 C:38I406 1.8 0.1 1.0
C24 C:38I406 2.8 97.8 1.0
C26 C:38I406 2.8 82.0 1.0
CL2 C:38I406 3.3 86.4 1.0
C23 C:38I406 4.1 85.3 1.0
C27 C:38I406 4.1 69.9 1.0
C22 C:38I406 4.6 69.6 1.0
CD C:PRO203 4.9 22.8 1.0

Reference:

A.Golebiowski, D.Whitehouse, R.P.Beckett, M.Van Zandt, M.K.Ji, T.R.Ryder, E.Jagdmann, M.Andreoli, Y.Lee, R.Sheeler, B.Conway, J.Olczak, M.Mazur, W.Czestkowski, W.Piotrowska, A.Cousido-Siah, F.X.Ruiz, A.Mitschler, A.Podjarny, H.Schroeter. Synthesis of Quaternary Alpha-Amino Acid-Based Arginase Inhibitors Via the Ugi Reaction. Bioorg.Med.Chem.Lett. V. 23 4837 2013.
ISSN: ISSN 0960-894X
PubMed: 23886684
DOI: 10.1016/J.BMCL.2013.06.092
Page generated: Sun Jul 21 17:07:37 2024

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