Manganese in PDB 5jfr: Potent, Reversible METAP2 Inhibitors Via Fragment Based Drug Discovery

All present enzymatic activity of Potent, Reversible METAP2 Inhibitors Via Fragment Based Drug Discovery:
3.4.11.18;

The structure of Potent, Reversible METAP2 Inhibitors Via Fragment Based Drug Discovery, PDB code: 5jfr was solved by D.R.Dougan, J.D.Lawson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.60
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	89.644, 100.816, 99.445, 90.00, 90.00, 90.00
R / Rfree (%)	13.6 / 17.1

The structure of Potent, Reversible METAP2 Inhibitors Via Fragment Based Drug Discovery also contains other interesting chemical elements:

Fluorine

(F)

1 atom

The binding sites of Manganese atom in the Potent, Reversible METAP2 Inhibitors Via Fragment Based Drug Discovery (pdb code 5jfr). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Potent, Reversible METAP2 Inhibitors Via Fragment Based Drug Discovery, PDB code: 5jfr:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Potent, Reversible METAP2 Inhibitors Via Fragment Based Drug Discovery


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Potent, Reversible METAP2 Inhibitors Via Fragment Based Drug Discovery within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:18.1 occ:1.00 OD1 A:ASP251 2.0 17.1 1.0 OE2 A:GLU459 2.1 19.0 1.0 OD1 A:ASP262 2.1 20.5 1.0 O A:HOH642 2.1 23.9 1.0 OD2 A:ASP251 2.2 19.1 1.0 O A:HOH609 2.3 22.6 1.0 CG A:ASP251 2.5 18.5 1.0 CD A:GLU459 3.0 22.0 1.0 CG A:ASP262 3.1 20.2 1.0 OE1 A:GLU459 3.3 20.0 1.0 OD2 A:ASP262 3.4 21.1 1.0 MN A:MN502 3.4 21.3 1.0 N16 A:6KP505 4.0 25.3 1.0 OE2 A:GLU364 4.0 24.6 1.0 CZ A:PHE219 4.0 19.3 1.0 CB A:ASP251 4.0 18.2 1.0 NE2 A:GLN457 4.0 18.6 1.0 CE1 A:PHE219 4.3 19.5 1.0 O A:HOH643 4.3 34.2 1.0 CG A:GLU459 4.3 20.8 1.0 N15 A:6KP505 4.4 26.4 1.0 O A:HOH822 4.4 32.3 1.0 O A:HOH868 4.4 29.9 1.0 CB A:ASP262 4.4 19.6 1.0 N A:CYS263 4.6 18.3 1.0 CB A:ALA264 4.6 17.9 1.0 C A:ASP262 4.7 19.6 1.0 CD A:GLU364 4.7 24.1 1.0 CA A:ASP262 4.7 18.1 1.0 OE1 A:GLU364 4.7 24.7 1.0 CB A:GLU459 4.9 17.9 1.0 CE2 A:PHE219 4.9 21.1 1.0 CA A:ASP251 4.9 17.9 1.0

Manganese binding site 2 out of 2 in the Potent, Reversible METAP2 Inhibitors Via Fragment Based Drug Discovery


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Potent, Reversible METAP2 Inhibitors Via Fragment Based Drug Discovery within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn502 b:21.3 occ:1.00 O A:HOH642 2.1 23.9 1.0 NE2 A:HIS331 2.1 21.8 1.0 OD2 A:ASP262 2.2 21.1 1.0 OE1 A:GLU459 2.2 20.0 1.0 OE1 A:GLU364 2.3 24.7 1.0 N15 A:6KP505 2.3 26.4 1.0 CE1 A:HIS331 3.0 26.1 1.0 CD A:GLU364 3.1 24.1 1.0 CG A:ASP262 3.1 20.2 1.0 CD2 A:HIS331 3.2 24.4 1.0 N16 A:6KP505 3.2 25.3 1.0 CD A:GLU459 3.3 22.0 1.0 C14 A:6KP505 3.4 33.9 1.0 OE2 A:GLU364 3.4 24.6 1.0 MN A:MN501 3.4 18.1 1.0 OD1 A:ASP262 3.5 20.5 1.0 OE2 A:GLU459 3.7 19.0 1.0 CB A:ALA362 3.9 24.3 1.0 O A:HOH609 4.0 22.6 1.0 O A:HOH820 4.1 54.1 1.0 ND1 A:HIS331 4.2 27.7 1.0 CG A:GLU364 4.3 24.7 1.0 CG A:HIS331 4.3 27.3 1.0 CB A:ASP262 4.3 19.6 1.0 O A:HOH822 4.4 32.3 1.0 C18 A:6KP505 4.4 30.4 1.0 C13 A:6KP505 4.5 28.3 1.0 CG A:GLU459 4.6 20.8 1.0

C.Mcbride, Z.Cheruvallath, M.Komandla, M.Tang, P.Farrell, J.D.Lawson, D.Vanderpool, Y.Wu, D.R.Dougan, A.Plonowski, C.Holub, C.Larson. Discovery of Potent, Reversible METAP2 Inhibitors Via Fragment Based Drug Discovery and Structure Based Drug Design-Part 2. Bioorg.Med.Chem.Lett. V. 26 2779 2016.
ISSN: ESSN 1464-3405
PubMed: 27136719
DOI: 10.1016/J.BMCL.2016.04.072