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Fluorine in PDB 7a16: Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor GSK2229238A (Compound 43)

Enzymatic activity of Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor GSK2229238A (Compound 43)

All present enzymatic activity of Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor GSK2229238A (Compound 43):
3.4.11.18;

Protein crystallography data

The structure of Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor GSK2229238A (Compound 43), PDB code: 7a16 was solved by J.H.Thorpe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.32 / 1.90
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 89.891, 100.891, 99.608, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 21.6

Other elements in 7a16:

The structure of Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor GSK2229238A (Compound 43) 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 GSK2229238A (Compound 43) (pdb code 7a16). 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 GSK2229238A (Compound 43), PDB code: 7a16:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 7a16

Go back to Fluorine Binding Sites List in 7a16
Fluorine binding site 1 out of 2 in the Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor GSK2229238A (Compound 43)


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 GSK2229238A (Compound 43) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F508

b:23.9
occ:1.00
F14 A:HZE508 0.0 23.9 1.0
C1 A:HZE508 1.4 24.9 1.0
C4 A:HZE508 2.4 24.4 1.0
C2 A:HZE508 2.4 23.9 1.0
F15 A:HZE508 2.7 21.7 1.0
CD1 A:TYR444 3.2 22.6 1.0
CB A:ALA414 3.4 18.1 1.0
CG A:TYR444 3.5 21.3 1.0
C3 A:HZE508 3.6 20.9 1.0
C5 A:HZE508 3.6 22.6 1.0
CB A:MET384 3.7 19.1 1.0
CB A:TYR444 3.7 19.1 1.0
O A:TYR383 3.8 20.6 1.0
CE1 A:TYR444 3.8 21.4 1.0
C A:TYR383 3.9 21.6 1.0
CB A:HIS382 4.0 15.5 1.0
C6 A:HZE508 4.1 22.0 1.0
N A:TYR383 4.1 16.5 1.0
CD2 A:TYR444 4.3 21.6 1.0
N A:MET384 4.4 18.5 1.0
CA A:TYR383 4.4 16.5 1.0
SD A:MET384 4.5 22.0 1.0
C A:HIS382 4.5 19.6 1.0
CA A:ALA414 4.5 18.1 1.0
CZ A:TYR444 4.6 24.6 1.0
CA A:MET384 4.7 17.7 1.0
CG A:MET384 4.7 20.8 1.0
CE A:MET384 4.7 19.3 1.0
CD2 A:HIS382 4.7 18.6 1.0
CE2 A:TYR444 4.8 22.0 1.0
CA A:HIS382 4.8 16.6 1.0
CG A:HIS382 4.8 17.8 1.0
O A:HIS382 5.0 17.8 1.0
C9 A:HZE508 5.0 20.5 1.0

Fluorine binding site 2 out of 2 in 7a16

Go back to Fluorine Binding Sites List in 7a16
Fluorine binding site 2 out of 2 in the Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor GSK2229238A (Compound 43)


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 GSK2229238A (Compound 43) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F508

b:21.7
occ:1.00
F15 A:HZE508 0.0 21.7 1.0
C2 A:HZE508 1.3 23.9 1.0
C3 A:HZE508 2.3 20.9 1.0
C1 A:HZE508 2.4 24.9 1.0
F14 A:HZE508 2.7 23.9 1.0
CB A:ALA414 3.0 18.1 1.0
CD2 A:HIS382 3.3 18.6 1.0
CD A:PRO220 3.3 19.7 1.0
CB A:PHE219 3.6 17.3 1.0
C6 A:HZE508 3.6 22.0 1.0
C4 A:HZE508 3.6 24.4 1.0
CG A:HIS382 3.9 17.8 1.0
CB A:HIS382 4.0 15.5 1.0
C5 A:HZE508 4.1 22.6 1.0
CG A:PRO220 4.2 23.2 1.0
N A:PRO220 4.3 17.8 1.0
NE2 A:HIS382 4.3 18.7 1.0
CA A:ALA414 4.4 18.1 1.0
CG A:PHE219 4.5 17.4 1.0
CA A:PHE219 4.5 15.9 1.0
CD1 A:PHE219 4.7 17.6 1.0
O A:HOH889 4.7 21.6 1.0
O A:HOH758 4.8 17.4 1.0
C A:PHE219 4.8 19.0 1.0
C A:ALA414 4.8 20.0 1.0
O A:PHE415 4.8 17.6 1.0
N7 A:HZE508 4.9 22.5 1.0
CB A:PRO220 4.9 18.9 1.0
N A:PHE415 4.9 17.7 1.0
O A:TYR383 4.9 20.6 1.0
CA A:HIS382 5.0 16.6 1.0

Reference:

D.J.Hirst, M.Brandt, G.Bruton, E.Christodoulou, L.Cutler, N.Deeks, J.D.Goodacre, T.Jack, M.Lindon, A.Miah, K.Page, N.Parr, L.Shukla, M.Sims, P.Thomas, J.Thorpe, D.S.Holmes. Structure-Based Optimisation of Orally Active & Reversible Metap-2 Inhibitors Maintaining A Tight 'Molecular Budget'. Bioorg.Med.Chem.Lett. V. 30 27533 2020.
ISSN: ESSN 1464-3405
PubMed: 32919012
DOI: 10.1016/J.BMCL.2020.127533
Page generated: Tue Jul 15 18:26:05 2025

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