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Fluorine 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:

Manganese (Mn) 2 atoms

Fluorine Binding Sites:

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

Fluorine binding site 1 out of 2 in 6qei

Go back to Fluorine Binding Sites List in 6qei
Fluorine 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 Fluorine with other atoms in the F 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:F505

b:38.3
occ:1.00
 F14 A:HZE505 0.0 38.3 1.0
C1 A:HZE505 1.3 36.0 1.0
C4 A:HZE505 2.3 35.6 1.0
C2 A:HZE505 2.3 36.2 1.0
F15 A:HZE505 2.7 34.5 1.0
CD2 A:TYR444 3.2 33.9 1.0
CB A:ALA414 3.3 27.8 1.0
CG A:TYR444 3.4 33.2 1.0
C5 A:HZE505 3.6 36.9 1.0
C3 A:HZE505 3.6 37.5 1.0
CB A:MET384 3.7 27.3 1.0
CB A:TYR444 3.8 30.0 1.0
CE2 A:TYR444 3.8 34.4 1.0
O A:TYR383 3.8 27.3 1.0
C A:TYR383 4.0 29.8 1.0
CB A:HIS382 4.0 24.5 1.0
C6 A:HZE505 4.1 37.1 1.0
N A:TYR383 4.2 27.0 1.0
CD1 A:TYR444 4.3 35.0 1.0
N A:MET384 4.4 27.1 1.0
CA A:ALA414 4.4 27.6 1.0
SD A:MET384 4.5 31.8 1.0
C A:HIS382 4.5 29.5 1.0
CA A:TYR383 4.5 27.1 1.0
CZ A:TYR444 4.5 38.8 1.0
CG A:MET384 4.6 29.3 1.0
CE A:MET384 4.6 28.4 1.0
CA A:MET384 4.6 26.4 1.0
CD2 A:HIS382 4.7 28.6 1.0
CE1 A:TYR444 4.8 34.6 1.0
CG A:HIS382 4.8 27.6 1.0
CA A:HIS382 4.8 25.6 1.0
C9 A:HZE505 4.9 36.5 1.0
O A:HIS382 5.0 28.7 1.0

Fluorine binding site 2 out of 2 in 6qei

Go back to Fluorine Binding Sites List in 6qei
Fluorine 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 Fluorine with other atoms in the F 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:F505

b:34.5
occ:1.00
 F15 A:HZE505 0.0 34.5 1.0
C2 A:HZE505 1.3 36.2 1.0
C3 A:HZE505 2.3 37.5 1.0
C1 A:HZE505 2.3 36.0 1.0
F14 A:HZE505 2.7 38.3 1.0
CB A:ALA414 3.0 27.8 1.0
CD2 A:HIS382 3.1 28.6 1.0
CD A:PRO220 3.3 28.1 1.0
C6 A:HZE505 3.6 37.1 1.0
C4 A:HZE505 3.6 35.6 1.0
CB A:PHE219 3.7 26.9 1.0
CG A:HIS382 3.8 27.6 1.0
CB A:HIS382 4.0 24.5 1.0
C5 A:HZE505 4.1 36.9 1.0
CG A:PRO220 4.1 32.6 1.0
NE2 A:HIS382 4.1 28.5 1.0
N A:PRO220 4.3 26.7 1.0
CA A:ALA414 4.4 27.6 1.0
CG A:PHE219 4.6 27.7 1.0
CA A:PHE219 4.6 25.2 1.0
CD1 A:PHE219 4.8 29.4 1.0
C A:ALA414 4.8 31.3 1.0
O A:HOH681 4.8 27.2 1.0
N7 A:HZE505 4.8 36.6 1.0
O A:HOH774 4.8 37.6 1.0
C A:PHE219 4.9 27.6 1.0
N A:PHE415 4.9 27.6 1.0
CA A:HIS382 4.9 25.6 1.0
O A:PHE415 4.9 29.9 1.0
O A:TYR383 5.0 27.3 1.0
CB A:PRO220 5.0 27.5 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: Tue Jul 15 15:00:39 2025

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