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Fluorine in PDB 6qed: Crystal Structure of Human Methionine Aminopeptidase-2 in Complex; with An Inhibitor (S)-3-Hydroxy-2-Oxo-1-(2-Oxo-1,2,3,4-Tetrahydro- Quinolin-6-Yl)-Pyrrolidine-3-Carboxylic Acid 3-Chloro-5-Fluoro- Benzylamide

Enzymatic activity of Crystal Structure of Human Methionine Aminopeptidase-2 in Complex; with An Inhibitor (S)-3-Hydroxy-2-Oxo-1-(2-Oxo-1,2,3,4-Tetrahydro- Quinolin-6-Yl)-Pyrrolidine-3-Carboxylic Acid 3-Chloro-5-Fluoro- Benzylamide

All present enzymatic activity of Crystal Structure of Human Methionine Aminopeptidase-2 in Complex; with An Inhibitor (S)-3-Hydroxy-2-Oxo-1-(2-Oxo-1,2,3,4-Tetrahydro- Quinolin-6-Yl)-Pyrrolidine-3-Carboxylic Acid 3-Chloro-5-Fluoro- Benzylamide:
3.4.11.18;

Protein crystallography data

The structure of Crystal Structure of Human Methionine Aminopeptidase-2 in Complex; with An Inhibitor (S)-3-Hydroxy-2-Oxo-1-(2-Oxo-1,2,3,4-Tetrahydro- Quinolin-6-Yl)-Pyrrolidine-3-Carboxylic Acid 3-Chloro-5-Fluoro- Benzylamide, PDB code: 6qed 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) 44.70 / 1.80
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 89.300, 99.670, 101.080, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 19.8

Other elements in 6qed:

The structure of Crystal Structure of Human Methionine Aminopeptidase-2 in Complex; with An Inhibitor (S)-3-Hydroxy-2-Oxo-1-(2-Oxo-1,2,3,4-Tetrahydro- Quinolin-6-Yl)-Pyrrolidine-3-Carboxylic Acid 3-Chloro-5-Fluoro- Benzylamide also contains other interesting chemical elements:

Manganese (Mn) 2 atoms
Chlorine (Cl) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Human Methionine Aminopeptidase-2 in Complex; with An Inhibitor (S)-3-Hydroxy-2-Oxo-1-(2-Oxo-1,2,3,4-Tetrahydro- Quinolin-6-Yl)-Pyrrolidine-3-Carboxylic Acid 3-Chloro-5-Fluoro- Benzylamide (pdb code 6qed). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total only one binding site of Fluorine was determined in the Crystal Structure of Human Methionine Aminopeptidase-2 in Complex; with An Inhibitor (S)-3-Hydroxy-2-Oxo-1-(2-Oxo-1,2,3,4-Tetrahydro- Quinolin-6-Yl)-Pyrrolidine-3-Carboxylic Acid 3-Chloro-5-Fluoro- Benzylamide, PDB code: 6qed:

Fluorine binding site 1 out of 1 in 6qed

Go back to Fluorine Binding Sites List in 6qed
Fluorine binding site 1 out of 1 in the Crystal Structure of Human Methionine Aminopeptidase-2 in Complex; with An Inhibitor (S)-3-Hydroxy-2-Oxo-1-(2-Oxo-1,2,3,4-Tetrahydro- Quinolin-6-Yl)-Pyrrolidine-3-Carboxylic Acid 3-Chloro-5-Fluoro- Benzylamide


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 (S)-3-Hydroxy-2-Oxo-1-(2-Oxo-1,2,3,4-Tetrahydro- Quinolin-6-Yl)-Pyrrolidine-3-Carboxylic Acid 3-Chloro-5-Fluoro- Benzylamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F506

b:35.1
occ:1.00
 F20 A:HZK506 0.0 35.1 1.0
C5 A:HZK506 1.3 33.3 1.0
C6 A:HZK506 2.4 32.9 1.0
C4 A:HZK506 2.4 32.3 1.0
CB A:ALA414 3.2 22.5 1.0
CB A:HIS382 3.5 19.9 1.0
C1 A:HZK506 3.6 33.9 1.0
C3 A:HZK506 3.6 37.8 1.0
CD2 A:TYR444 3.7 29.2 1.0
CG A:TYR444 3.8 28.9 1.0
CB A:TYR444 3.8 26.4 1.0
CD2 A:HIS382 3.9 24.4 1.0
O A:TYR383 4.0 24.0 1.0
CG A:HIS382 4.1 22.6 1.0
N A:TYR383 4.1 21.5 1.0
C2 A:HZK506 4.1 33.9 1.0
C A:TYR383 4.3 23.6 1.0
C A:HIS382 4.3 24.5 1.0
CB A:MET384 4.3 23.0 1.0
CA A:ALA414 4.4 22.0 1.0
CA A:HIS382 4.4 20.7 1.0
CE2 A:TYR444 4.5 30.2 1.0
CD1 A:TYR444 4.6 31.7 1.0
CA A:TYR383 4.7 21.3 1.0
C19 A:HZK506 4.9 34.9 1.0
N A:MET384 4.9 22.2 1.0
SD A:MET384 4.9 28.0 1.0
O A:HIS382 4.9 23.9 1.0
CD A:PRO220 4.9 22.1 1.0
O A:PHE415 5.0 22.2 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 15:00:22 2025

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