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Fluorine in PDB 5mu6: Human N-Myristoyltransferase (NMT1) with Myristoyl-Coa and Imp-1088 Inhibitor Bound

Enzymatic activity of Human N-Myristoyltransferase (NMT1) with Myristoyl-Coa and Imp-1088 Inhibitor Bound

All present enzymatic activity of Human N-Myristoyltransferase (NMT1) with Myristoyl-Coa and Imp-1088 Inhibitor Bound:
2.3.1.97;

Protein crystallography data

The structure of Human N-Myristoyltransferase (NMT1) with Myristoyl-Coa and Imp-1088 Inhibitor Bound, PDB code: 5mu6 was solved by I.Perez-Dorado, A.S.Bell, E.W.Tate, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 72.18 / 1.88
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.730, 180.730, 58.990, 90.00, 90.00, 90.00
R / Rfree (%) 20.4 / 24.7

Other elements in 5mu6:

The structure of Human N-Myristoyltransferase (NMT1) with Myristoyl-Coa and Imp-1088 Inhibitor Bound also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Human N-Myristoyltransferase (NMT1) with Myristoyl-Coa and Imp-1088 Inhibitor Bound (pdb code 5mu6). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Human N-Myristoyltransferase (NMT1) with Myristoyl-Coa and Imp-1088 Inhibitor Bound, PDB code: 5mu6:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 5mu6

Go back to Fluorine Binding Sites List in 5mu6
Fluorine binding site 1 out of 4 in the Human N-Myristoyltransferase (NMT1) with Myristoyl-Coa and Imp-1088 Inhibitor Bound


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Human N-Myristoyltransferase (NMT1) with Myristoyl-Coa and Imp-1088 Inhibitor Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F505

b:11.8
occ:1.00
 FAY A:KFK505 0.0 11.8 1.0
CAN A:KFK505 1.3 8.8 1.0
CAM A:KFK505 2.4 9.9 1.0
CAO A:KFK505 2.4 9.3 1.0
FAX A:KFK505 2.7 9.5 1.0
N A:ALA452 3.1 7.0 1.0
CB A:ASN451 3.1 8.5 1.0
C A:ASN451 3.2 7.5 1.0
CA A:ALA452 3.4 6.3 1.0
C A:ALA452 3.4 8.2 1.0
O A:HOH617 3.6 19.7 1.0
CAI A:KFK505 3.6 13.1 1.0
O A:ASN451 3.6 10.9 1.0
CAP A:KFK505 3.6 10.1 1.0
CA A:ASN451 3.7 6.9 1.0
O A:ALA452 3.8 9.8 1.0
N A:LEU453 3.8 11.8 1.0
CD2 A:TYR420 3.9 5.4 1.0
CB A:TYR296 4.2 11.6 1.0
CAQ A:KFK505 4.2 7.6 1.0
CE2 A:TYR420 4.2 7.7 1.0
O A:HOH780 4.3 18.5 1.0
CG A:ASN451 4.3 10.9 1.0
CG A:LEU453 4.4 10.3 1.0
O A:TRP297 4.5 11.5 1.0
CA A:LEU453 4.6 7.6 1.0
OAH A:KFK505 4.7 10.8 1.0
CD2 A:LEU453 4.8 12.8 1.0
CB A:ALA452 4.9 10.1 1.0
ND2 A:ASN451 4.9 9.3 1.0
CA A:TYR296 4.9 9.4 1.0
CG A:TYR420 4.9 7.0 1.0

Fluorine binding site 2 out of 4 in 5mu6

Go back to Fluorine Binding Sites List in 5mu6
Fluorine binding site 2 out of 4 in the Human N-Myristoyltransferase (NMT1) with Myristoyl-Coa and Imp-1088 Inhibitor Bound


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Human N-Myristoyltransferase (NMT1) with Myristoyl-Coa and Imp-1088 Inhibitor Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F505

b:9.5
occ:1.00
 FAX A:KFK505 0.0 9.5 1.0
CAM A:KFK505 1.4 9.9 1.0
CAN A:KFK505 2.4 8.8 1.0
CAI A:KFK505 2.4 13.1 1.0
OAH A:KFK505 2.7 10.8 1.0
FAY A:KFK505 2.7 11.8 1.0
CB A:ASN451 3.2 8.5 1.0
CE1 A:HIS298 3.3 10.6 1.0
CB A:TYR296 3.4 11.6 1.0
CAG A:KFK505 3.4 9.9 1.0
CG A:ASN451 3.5 10.9 1.0
ND1 A:HIS298 3.6 7.7 1.0
CAO A:KFK505 3.7 9.3 1.0
CAQ A:KFK505 3.7 7.6 1.0
OD1 A:ASN451 3.8 9.5 1.0
CG A:TYR296 3.9 8.8 1.0
ND2 A:ASN451 4.0 9.3 1.0
CD1 A:TYR296 4.0 12.6 1.0
CAP A:KFK505 4.1 10.1 1.0
O A:TRP297 4.2 11.5 1.0
CE2 A:TYR420 4.2 7.7 1.0
CAF A:KFK505 4.3 7.6 1.0
CA A:ASN451 4.3 6.9 1.0
NE2 A:HIS298 4.5 9.2 1.0
CA A:TYR296 4.6 9.4 1.0
N A:ALA452 4.6 7.0 1.0
N A:TRP297 4.7 9.0 1.0
C A:ASN451 4.7 7.5 1.0
CD2 A:TYR420 4.8 5.4 1.0
CD2 A:TYR296 4.8 10.4 1.0
C A:TYR296 4.8 9.1 1.0
CG A:HIS298 4.9 6.4 1.0
C A:TRP297 4.9 10.2 1.0
CZ A:TYR420 5.0 9.9 1.0

Fluorine binding site 3 out of 4 in 5mu6

Go back to Fluorine Binding Sites List in 5mu6
Fluorine binding site 3 out of 4 in the Human N-Myristoyltransferase (NMT1) with Myristoyl-Coa and Imp-1088 Inhibitor Bound


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Human N-Myristoyltransferase (NMT1) with Myristoyl-Coa and Imp-1088 Inhibitor Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F505

b:10.6
occ:1.00
 FAY B:KFK505 0.0 10.6 1.0
CAN B:KFK505 1.3 9.6 1.0
CAO B:KFK505 2.4 10.7 1.0
CAM B:KFK505 2.4 7.2 1.0
FAX B:KFK505 2.7 10.2 1.0
N B:ALA452 3.1 6.2 1.0
CB B:ASN451 3.2 7.5 1.0
C B:ASN451 3.2 8.3 1.0
CA B:ALA452 3.4 6.2 1.0
C B:ALA452 3.4 8.7 1.0
O B:ASN451 3.6 9.0 1.0
CAP B:KFK505 3.6 9.1 1.0
CAI B:KFK505 3.7 7.5 1.0
N B:LEU453 3.7 7.8 1.0
O B:ALA452 3.8 10.7 1.0
CA B:ASN451 3.8 8.7 1.0
CD2 B:TYR420 3.9 6.5 1.0
O B:HOH768 4.0 21.4 1.0
CB B:TYR296 4.2 9.2 1.0
CAQ B:KFK505 4.2 9.7 1.0
CE2 B:TYR420 4.2 7.4 1.0
CG B:LEU453 4.3 8.0 1.0
CG B:ASN451 4.4 9.6 1.0
O B:TRP297 4.5 11.0 1.0
CA B:LEU453 4.6 8.9 1.0
OAH B:KFK505 4.8 7.8 1.0
CD2 B:LEU453 4.8 10.4 1.0
O B:HOH718 4.9 11.7 1.0
CB B:ALA452 4.9 8.7 1.0
CA B:TYR296 4.9 9.6 1.0
CB B:LEU453 5.0 10.7 1.0
CG B:TYR420 5.0 10.2 1.0

Fluorine binding site 4 out of 4 in 5mu6

Go back to Fluorine Binding Sites List in 5mu6
Fluorine binding site 4 out of 4 in the Human N-Myristoyltransferase (NMT1) with Myristoyl-Coa and Imp-1088 Inhibitor Bound


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Human N-Myristoyltransferase (NMT1) with Myristoyl-Coa and Imp-1088 Inhibitor Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F505

b:10.2
occ:1.00
 FAX B:KFK505 0.0 10.2 1.0
CAM B:KFK505 1.3 7.2 1.0
CAN B:KFK505 2.4 9.6 1.0
CAI B:KFK505 2.4 7.5 1.0
FAY B:KFK505 2.7 10.6 1.0
OAH B:KFK505 2.7 7.8 1.0
CB B:ASN451 3.2 7.5 1.0
CE1 B:HIS298 3.4 10.9 1.0
CB B:TYR296 3.4 9.2 1.0
CG B:ASN451 3.5 9.6 1.0
CAG B:KFK505 3.5 10.3 1.0
CAO B:KFK505 3.6 10.7 1.0
CAQ B:KFK505 3.7 9.7 1.0
ND1 B:HIS298 3.7 9.6 1.0
OD1 B:ASN451 3.9 9.1 1.0
CG B:TYR296 3.9 10.6 1.0
ND2 B:ASN451 3.9 10.8 1.0
CAP B:KFK505 4.1 9.1 1.0
O B:TRP297 4.1 11.0 1.0
CD2 B:TYR296 4.1 11.6 1.0
CE2 B:TYR420 4.2 7.4 1.0
CA B:ASN451 4.3 8.7 1.0
CAF B:KFK505 4.4 10.6 1.0
NE2 B:HIS298 4.5 11.8 1.0
N B:ALA452 4.6 6.2 1.0
CA B:TYR296 4.6 9.6 1.0
N B:TRP297 4.6 8.3 1.0
C B:ASN451 4.7 8.3 1.0
CD2 B:TYR420 4.8 6.5 1.0
C B:TYR296 4.8 10.8 1.0
CD1 B:TYR296 4.9 11.8 1.0
C B:TRP297 4.9 7.1 1.0
CZ B:TYR420 4.9 6.4 1.0
CG B:HIS298 4.9 10.3 1.0
OH B:TYR420 5.0 10.5 1.0

Reference:

A.Mousnier, A.S.Bell, D.P.Swieboda, J.Morales-Sanfrutos, I.Perez-Dorado, J.A.Brannigan, J.Newman, M.Ritzefeld, J.A.Hutton, A.Guedan, A.S.Asfor, S.W.Robinson, I.Hopkins-Navratilova, A.J.Wilkinson, S.L.Johnston, R.J.Leatherbarrow, T.J.Tuthill, R.Solari, E.W.Tate. Fragment-Derived Inhibitors of Human N-Myristoyltransferase Block Capsid Assembly and Replication of the Common Cold Virus. Nat Chem V. 10 599 2018.
ISSN: ESSN 1755-4349
PubMed: 29760414
DOI: 10.1038/S41557-018-0039-2
Page generated: Sun Dec 13 12:28:22 2020

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