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Manganese in PDB 6qei: Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor 5,6-Difluoro-3-(2-Isopropoxy-4-Piperazin-1-Yl-Phenyl)- 1H-Indole-2-Carboxylic Acid Amide

Enzymatic activity of Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor 5,6-Difluoro-3-(2-Isopropoxy-4-Piperazin-1-Yl-Phenyl)- 1H-Indole-2-Carboxylic Acid Amide

All present enzymatic activity of Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor 5,6-Difluoro-3-(2-Isopropoxy-4-Piperazin-1-Yl-Phenyl)- 1H-Indole-2-Carboxylic Acid Amide:
3.4.11.18;

Protein crystallography data

The structure of Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor 5,6-Difluoro-3-(2-Isopropoxy-4-Piperazin-1-Yl-Phenyl)- 1H-Indole-2-Carboxylic Acid Amide, PDB code: 6qei was solved by D.Musil, T.Heinrich, M.Lehmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.46 / 1.80
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 89.808, 99.784, 100.819, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 20.9

Other elements in 6qei:

The structure of Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor 5,6-Difluoro-3-(2-Isopropoxy-4-Piperazin-1-Yl-Phenyl)- 1H-Indole-2-Carboxylic Acid Amide also contains other interesting chemical elements:

Fluorine (F) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor 5,6-Difluoro-3-(2-Isopropoxy-4-Piperazin-1-Yl-Phenyl)- 1H-Indole-2-Carboxylic Acid Amide (pdb code 6qei). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor 5,6-Difluoro-3-(2-Isopropoxy-4-Piperazin-1-Yl-Phenyl)- 1H-Indole-2-Carboxylic Acid Amide, PDB code: 6qei:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 6qei

Go back to Manganese Binding Sites List in 6qei
Manganese binding site 1 out of 2 in the Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor 5,6-Difluoro-3-(2-Isopropoxy-4-Piperazin-1-Yl-Phenyl)- 1H-Indole-2-Carboxylic Acid Amide


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor 5,6-Difluoro-3-(2-Isopropoxy-4-Piperazin-1-Yl-Phenyl)- 1H-Indole-2-Carboxylic Acid Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn506

b:33.7
occ:1.00
 OD2 A:ASP262 2.1 32.1 1.0
NE2 A:HIS331 2.3 33.6 1.0
OE2 A:GLU459 2.3 25.9 1.0
OE2 A:GLU364 2.3 33.2 1.0
O A:HOH605 2.3 34.2 1.0
O12 A:HZE505 2.4 38.1 1.0
CD A:GLU364 3.1 42.7 1.0
CG A:ASP262 3.1 28.1 1.0
CE1 A:HIS331 3.2 33.5 1.0
CD A:GLU459 3.3 28.3 1.0
CD2 A:HIS331 3.4 34.5 1.0
MN A:MN507 3.4 30.4 1.0
OE1 A:GLU364 3.4 31.0 1.0
OD1 A:ASP262 3.5 29.0 1.0
C10 A:HZE505 3.5 40.4 1.0
OE1 A:GLU459 3.7 28.1 1.0
CB A:ALA362 3.9 34.6 1.0
O A:HOH745 3.9 28.5 1.0
N11 A:HZE505 4.1 41.2 1.0
CG A:GLU364 4.2 35.6 1.0
CB A:ASP262 4.3 30.3 1.0
ND1 A:HIS331 4.4 34.4 1.0
O A:HOH747 4.4 35.7 1.0
O A:HOH744 4.4 45.1 1.0
CG A:HIS331 4.4 34.2 1.0
CG A:GLU459 4.6 32.4 1.0
C8 A:HZE505 4.7 38.5 1.0
N7 A:HZE505 4.7 36.6 1.0
CB A:GLU364 5.0 33.0 1.0
CD1 A:ILE338 5.0 43.4 1.0

Manganese binding site 2 out of 2 in 6qei

Go back to Manganese Binding Sites List in 6qei
Manganese binding site 2 out of 2 in the Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor 5,6-Difluoro-3-(2-Isopropoxy-4-Piperazin-1-Yl-Phenyl)- 1H-Indole-2-Carboxylic Acid Amide


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor 5,6-Difluoro-3-(2-Isopropoxy-4-Piperazin-1-Yl-Phenyl)- 1H-Indole-2-Carboxylic Acid Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn507

b:30.4
occ:1.00
 OD1 A:ASP262 2.1 29.0 1.0
OE1 A:GLU459 2.1 28.1 1.0
O A:HOH605 2.2 34.2 1.0
OD1 A:ASP251 2.2 25.0 1.0
OD2 A:ASP251 2.3 27.8 1.0
O A:HOH745 2.5 28.5 1.0
CG A:ASP251 2.5 27.1 1.0
CD A:GLU459 3.0 28.3 1.0
CG A:ASP262 3.1 28.1 1.0
OE2 A:GLU459 3.2 25.9 1.0
OD2 A:ASP262 3.4 32.1 1.0
MN A:MN506 3.4 33.7 1.0
CZ A:PHE219 3.9 28.9 1.0
NE2 A:GLN457 4.0 28.0 1.0
CB A:ASP251 4.1 26.1 1.0
OE1 A:GLU364 4.1 31.0 1.0
O A:HOH774 4.3 37.6 1.0
CE1 A:PHE219 4.3 31.0 1.0
O A:HOH616 4.4 33.9 1.0
CG A:GLU459 4.4 32.4 1.0
O A:HOH747 4.4 35.7 1.0
CB A:ASP262 4.4 30.3 1.0
O12 A:HZE505 4.4 38.1 1.0
CB A:ALA264 4.5 24.7 1.0
N A:CYS263 4.6 28.9 1.0
C A:ASP262 4.7 32.4 1.0
CE2 A:PHE219 4.7 30.9 1.0
CA A:ASP262 4.8 28.6 1.0
CD A:GLU364 4.8 42.7 1.0
OE2 A:GLU364 4.8 33.2 1.0
CB A:GLU459 4.9 26.0 1.0
CA A:ASP251 4.9 24.5 1.0

Reference:

T.Heinrich, J.Seenisamy, B.Blume, J.Bomke, M.Calderini, U.Eckert, M.Friese-Hamim, R.Kohl, M.Lehmann, B.Leuthner, D.Musil, F.Rohdich, F.T.Zenke. Discovery and Structure-Based Optimization of Next-Generation Reversible Methionine Aminopeptidase-2 (Metap-2) Inhibitors. J.Med.Chem. V. 62 5025 2019.
ISSN: ISSN 0022-2623
PubMed: 30939017
DOI: 10.1021/ACS.JMEDCHEM.9B00041
Page generated: Sun Oct 6 05:56:22 2024

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