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Manganese 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:

Fluorine (F) 1 atom
Chlorine (Cl) 1 atom

Manganese Binding Sites:

The binding sites of Manganese 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 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 (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:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 6qed

Go back to Manganese Binding Sites List in 6qed
Manganese binding site 1 out of 2 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 Manganese with other atoms in the Mn 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:Mn507

b:29.6
occ:1.00
 OD2 A:ASP262 2.1 30.6 1.0
OE2 A:GLU364 2.2 30.5 1.0
OE2 A:GLU459 2.2 24.8 1.0
NE2 A:HIS331 2.2 26.1 1.0
O14 A:HZK506 2.4 32.5 1.0
O16 A:HZK506 2.9 33.9 1.0
CG A:ASP262 3.0 26.4 1.0
CD A:GLU364 3.0 43.7 1.0
CE1 A:HIS331 3.2 25.8 1.0
CD2 A:HIS331 3.2 28.4 1.0
CD A:GLU459 3.3 27.6 1.0
C13 A:HZK506 3.3 31.3 1.0
C12 A:HZK506 3.3 33.9 1.0
MN A:MN508 3.4 23.7 1.0
OD1 A:ASP262 3.4 23.8 1.0
OE1 A:GLU364 3.4 32.6 1.0
OE1 A:GLU459 3.6 22.6 1.0
CB A:ALA362 3.8 29.8 1.0
C15 A:HZK506 3.9 33.5 1.0
O18 A:HZK506 4.1 32.5 1.0
CG A:GLU364 4.3 34.6 1.0
CB A:ASP262 4.3 25.5 1.0
N9 A:HZK506 4.4 33.5 1.0
ND1 A:HIS331 4.4 27.6 1.0
CG A:HIS331 4.4 28.0 1.0
CG A:GLU459 4.6 24.5 1.0
C11 A:HZK506 4.7 32.0 1.0
NE2 A:HIS339 4.8 41.9 1.0
N17 A:HZK506 4.8 33.2 1.0
C23 A:HZK506 4.8 41.0 1.0
CB A:GLU364 4.8 30.3 1.0

Manganese binding site 2 out of 2 in 6qed

Go back to Manganese Binding Sites List in 6qed
Manganese binding site 2 out of 2 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 Manganese with other atoms in the Mn binding site number 2 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:Mn508

b:23.7
occ:1.00
 OD1 A:ASP262 2.0 23.8 1.0
OE1 A:GLU459 2.1 22.6 1.0
OD1 A:ASP251 2.2 21.3 1.0
OD2 A:ASP251 2.2 23.4 1.0
O14 A:HZK506 2.2 32.5 1.0
O18 A:HZK506 2.5 32.5 1.0
CG A:ASP251 2.5 19.4 1.0
CD A:GLU459 3.0 27.6 1.0
CG A:ASP262 3.0 26.4 1.0
C15 A:HZK506 3.2 33.5 1.0
C12 A:HZK506 3.2 33.9 1.0
OE2 A:GLU459 3.2 24.8 1.0
MN A:MN507 3.4 29.6 1.0
OD2 A:ASP262 3.4 30.6 1.0
CZ A:PHE219 4.0 25.5 1.0
NE2 A:GLN457 4.0 25.9 1.0
C11 A:HZK506 4.0 32.0 1.0
CB A:ASP251 4.0 17.1 1.0
OE1 A:GLU364 4.1 32.6 1.0
CE1 A:PHE219 4.3 24.8 1.0
CB A:ASP262 4.4 25.5 1.0
C13 A:HZK506 4.4 31.3 1.0
CG A:GLU459 4.4 24.5 1.0
N17 A:HZK506 4.4 33.2 1.0
CB A:ALA264 4.5 20.9 1.0
N A:CYS263 4.6 23.4 1.0
C A:ASP262 4.6 26.0 1.0
OE2 A:GLU364 4.6 30.5 1.0
CD A:GLU364 4.7 43.7 1.0
O16 A:HZK506 4.7 33.9 1.0
CA A:ASP262 4.7 23.9 1.0
CA A:ASP251 4.8 17.6 1.0
CB A:GLU459 4.9 20.9 1.0
CE2 A:PHE219 4.9 26.7 1.0
O A:CYS263 5.0 22.0 1.0
C A:CYS263 5.0 23.7 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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