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Fluorine in PDB 6mb1: Crystal Structure of N-Myristoyl Transferase (Nmt) From Plasmodium Vivax in Complex with Inhibitor Imp-1002

Enzymatic activity of Crystal Structure of N-Myristoyl Transferase (Nmt) From Plasmodium Vivax in Complex with Inhibitor Imp-1002

All present enzymatic activity of Crystal Structure of N-Myristoyl Transferase (Nmt) From Plasmodium Vivax in Complex with Inhibitor Imp-1002:
2.3.1.97;

Protein crystallography data

The structure of Crystal Structure of N-Myristoyl Transferase (Nmt) From Plasmodium Vivax in Complex with Inhibitor Imp-1002, PDB code: 6mb1 was solved by Seattle Structural Genomics Center For Infectious Disease, Seattlestructural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.560, 119.110, 176.080, 90.00, 90.00, 90.00
R / Rfree (%) 15.4 / 18.3

Other elements in 6mb1:

The structure of Crystal Structure of N-Myristoyl Transferase (Nmt) From Plasmodium Vivax in Complex with Inhibitor Imp-1002 also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of N-Myristoyl Transferase (Nmt) From Plasmodium Vivax in Complex with Inhibitor Imp-1002 (pdb code 6mb1). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of N-Myristoyl Transferase (Nmt) From Plasmodium Vivax in Complex with Inhibitor Imp-1002, PDB code: 6mb1:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 6mb1

Go back to Fluorine Binding Sites List in 6mb1
Fluorine binding site 1 out of 3 in the Crystal Structure of N-Myristoyl Transferase (Nmt) From Plasmodium Vivax in Complex with Inhibitor Imp-1002


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 N-Myristoyl Transferase (Nmt) From Plasmodium Vivax in Complex with Inhibitor Imp-1002 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:14.2
occ:1.00
 F19 A:JCY502 0.0 14.2 1.0
C18 A:JCY502 1.4 10.1 1.0
C17 A:JCY502 2.3 10.0 1.0
C20 A:JCY502 2.4 12.0 1.0
N A:ALA366 3.2 8.6 1.0
CB A:ASN365 3.3 7.9 1.0
C A:ASN365 3.4 11.8 1.0
C A:ALA366 3.5 6.2 1.0
CB A:TYR211 3.6 11.6 1.0
C16 A:JCY502 3.6 8.0 1.0
CA A:ALA366 3.6 7.8 1.0
C21 A:JCY502 3.6 11.8 1.0
O A:ALA366 3.6 9.0 1.0
CA A:ASN365 3.8 7.4 1.0
O A:ASN365 3.9 10.8 1.0
CD2 A:TYR334 3.9 9.0 1.0
CE2 A:TYR334 3.9 7.0 1.0
O A:HOH654 4.0 14.5 1.0
N A:LEU367 4.0 7.9 1.0
C15 A:JCY502 4.1 11.8 1.0
O A:TYR212 4.3 10.9 1.0
CG A:ASN365 4.3 10.8 1.0
CG A:LEU367 4.4 7.3 1.0
CA A:TYR211 4.5 9.8 1.0
CG A:TYR211 4.6 9.4 1.0
CD2 A:LEU367 4.6 9.1 1.0
O A:HOH665 4.6 18.3 1.0
ND2 A:ASN365 4.7 17.0 1.0
N A:TYR212 4.7 8.2 1.0
O22 A:JCY502 4.8 11.5 1.0
CA A:LEU367 4.8 8.0 1.0
CG A:TYR334 5.0 8.7 1.0
CZ A:TYR334 5.0 8.2 1.0
C23 A:JCY502 5.0 11.4 1.0

Fluorine binding site 2 out of 3 in 6mb1

Go back to Fluorine Binding Sites List in 6mb1
Fluorine binding site 2 out of 3 in the Crystal Structure of N-Myristoyl Transferase (Nmt) From Plasmodium Vivax in Complex with Inhibitor Imp-1002


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 N-Myristoyl Transferase (Nmt) From Plasmodium Vivax in Complex with Inhibitor Imp-1002 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:13.7
occ:1.00
 F19 B:JCY502 0.0 13.7 1.0
C18 B:JCY502 1.4 10.5 1.0
C17 B:JCY502 2.3 13.6 1.0
C20 B:JCY502 2.4 12.1 1.0
N B:ALA366 3.2 9.4 1.0
CB B:ASN365 3.3 11.0 1.0
C B:ASN365 3.4 13.0 1.0
C B:ALA366 3.5 7.8 1.0
C16 B:JCY502 3.6 10.3 1.0
CA B:ALA366 3.6 9.8 1.0
CB B:TYR211 3.6 11.2 1.0
O B:ALA366 3.6 9.7 1.0
C21 B:JCY502 3.6 13.1 1.0
O B:ASN365 3.8 13.1 1.0
CA B:ASN365 3.8 9.3 1.0
O B:HOH655 3.9 16.6 1.0
CD2 B:TYR334 3.9 9.8 1.0
N B:LEU367 4.0 8.0 1.0
CE2 B:TYR334 4.0 11.3 1.0
C15 B:JCY502 4.1 11.6 1.0
O B:TYR212 4.3 11.7 1.0
CG B:ASN365 4.3 12.6 1.0
CG B:LEU367 4.4 9.9 1.0
CA B:TYR211 4.6 10.9 1.0
O B:HOH714 4.6 18.3 1.0
CG B:TYR211 4.7 9.6 1.0
CD2 B:LEU367 4.7 10.0 1.0
ND2 B:ASN365 4.7 17.4 1.0
N B:TYR212 4.8 9.6 1.0
CA B:LEU367 4.8 8.5 1.0
O22 B:JCY502 4.8 15.6 1.0
CG B:TYR334 4.9 8.5 1.0
C23 B:JCY502 5.0 16.8 1.0

Fluorine binding site 3 out of 3 in 6mb1

Go back to Fluorine Binding Sites List in 6mb1
Fluorine binding site 3 out of 3 in the Crystal Structure of N-Myristoyl Transferase (Nmt) From Plasmodium Vivax in Complex with Inhibitor Imp-1002


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of N-Myristoyl Transferase (Nmt) From Plasmodium Vivax in Complex with Inhibitor Imp-1002 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F502

b:15.8
occ:1.00
 F19 C:JCY502 0.0 15.8 1.0
C18 C:JCY502 1.4 12.0 1.0
C17 C:JCY502 2.3 12.4 1.0
C20 C:JCY502 2.4 11.7 1.0
N C:ALA366 3.2 8.7 1.0
CB C:ASN365 3.2 8.2 1.0
C C:ASN365 3.4 12.2 1.0
C C:ALA366 3.4 7.6 1.0
O C:ALA366 3.5 11.1 1.0
C16 C:JCY502 3.6 12.1 1.0
CA C:ALA366 3.6 9.6 1.0
C21 C:JCY502 3.6 12.1 1.0
CB C:TYR211 3.7 10.2 1.0
CA C:ASN365 3.8 10.4 1.0
O C:HOH714 3.8 14.8 1.0
O C:ASN365 3.8 11.3 1.0
N C:LEU367 4.0 8.1 1.0
CD2 C:TYR334 4.0 8.9 1.0
CE2 C:TYR334 4.1 10.3 1.0
C15 C:JCY502 4.1 10.7 1.0
O C:TYR212 4.3 10.7 1.0
CG C:ASN365 4.3 13.1 1.0
CG C:LEU367 4.3 7.8 1.0
O C:HOH749 4.6 18.8 1.0
CD2 C:LEU367 4.6 9.5 1.0
CA C:TYR211 4.6 10.4 1.0
CG C:TYR211 4.7 11.6 1.0
N C:TYR212 4.7 10.0 1.0
CA C:LEU367 4.8 9.0 1.0
O22 C:JCY502 4.8 18.5 1.0
ND2 C:ASN365 4.9 20.2 1.0
OD1 C:ASN365 5.0 15.4 1.0

Reference:

A.C.Schlott, S.Mayclin, A.R.Reers, O.Coburn-Flynn, A.S.Bell, J.Green, E.Knuepfer, D.Charter, R.Bonnert, B.Campo, J.Burrows, S.Lyons-Abbott, B.L.Staker, C.W.Chung, P.J.Myler, D.A.Fidock, E.W.Tate, A.A.Holder. Structure-Guided Identification of Resistance Breaking Antimalarial N‐Myristoyltransferase Inhibitors. Cell Chem Biol V. 26 991 2019.
ISSN: ESSN 2451-9456
PubMed: 31080074
DOI: 10.1016/J.CHEMBIOL.2019.03.015
Page generated: Tue Jul 15 13:07:37 2025

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