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Fluorine in PDB 5gvm: Plasmodium Vivax Shmt Bound with Plp-Glycine and GS557

Protein crystallography data

The structure of Plasmodium Vivax Shmt Bound with Plp-Glycine and GS557, PDB code: 5gvm was solved by P.Chitnumsub, A.Jaruwat, U.Leartsakulpanich, G.Schwertz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.01 / 2.24
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 101.858, 58.790, 234.062, 90.00, 90.03, 90.00
R / Rfree (%) 24 / 29.7

Other elements in 5gvm:

The structure of Plasmodium Vivax Shmt Bound with Plp-Glycine and GS557 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS557 (pdb code 5gvm). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 9 binding sites of Fluorine where determined in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS557, PDB code: 5gvm:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Fluorine binding site 1 out of 9 in 5gvm

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Fluorine binding site 1 out of 9 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS557


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Plasmodium Vivax Shmt Bound with Plp-Glycine and GS557 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:23.2
occ:1.00
 F48 A:G57502 0.0 23.2 1.0
C35 A:G57502 1.3 23.3 1.0
F46 A:G57502 2.0 24.3 1.0
F47 A:G57502 2.2 25.2 1.0
C18 A:G57502 2.4 23.4 1.0
C17 A:G57502 2.7 22.9 1.0
O A:LYS355 3.2 25.3 1.0
C A:LYS355 3.4 24.0 1.0
N A:ASN356 3.4 23.2 1.0
CA A:ASN356 3.4 21.5 1.0
CB A:PRO367 3.6 33.9 1.0
C19 A:G57502 3.6 23.7 1.0
CG A:PRO367 3.7 34.6 1.0
C A:ASN356 3.8 22.3 1.0
N A:THR357 3.8 23.8 1.0
N9 A:G57502 4.0 24.4 1.0
CD A:LYS355 4.1 30.1 1.0
CG A:LYS355 4.1 28.1 1.0
CB A:LYS355 4.1 25.1 1.0
C16 A:G57502 4.2 22.8 1.0
CA A:LYS355 4.4 24.3 1.0
CG2 A:THR357 4.5 24.8 1.0
C8 A:G57502 4.5 23.8 1.0
O A:ASN356 4.6 22.6 1.0
C20 A:G57502 4.8 23.4 1.0
CB A:ASN356 4.8 20.2 1.0
CD A:PRO367 4.8 35.9 1.0
CA A:THR357 4.9 24.6 1.0
C21 A:G57502 5.0 23.4 1.0

Fluorine binding site 2 out of 9 in 5gvm

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Fluorine binding site 2 out of 9 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS557


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Plasmodium Vivax Shmt Bound with Plp-Glycine and GS557 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:25.2
occ:1.00
 F47 A:G57502 0.0 25.2 1.0
C35 A:G57502 1.3 23.3 1.0
F46 A:G57502 2.2 24.3 1.0
F48 A:G57502 2.2 23.2 1.0
C18 A:G57502 2.3 23.4 1.0
C19 A:G57502 2.9 23.7 1.0
CD A:LYS355 3.3 30.1 1.0
C17 A:G57502 3.4 22.9 1.0
NZ A:LYS355 3.4 33.7 1.0
CD2 B:TYR63 3.8 24.6 1.0
CE2 B:TYR63 3.8 24.2 1.0
CE A:LYS355 3.9 32.0 1.0
O A:CYS364 3.9 58.2 1.0
CG A:PRO367 4.0 34.6 1.0
CG A:LYS355 4.0 28.1 1.0
C20 A:G57502 4.2 23.4 1.0
CB A:PRO367 4.5 33.9 1.0
C16 A:G57502 4.5 22.8 1.0
CD A:PRO367 4.6 35.9 1.0
O A:LYS355 4.6 25.3 1.0
CB A:LYS355 4.7 25.1 1.0
C21 A:G57502 4.8 23.4 1.0
CB A:CYS364 4.9 52.0 1.0
C A:LYS355 4.9 24.0 1.0
C A:CYS364 4.9 57.3 1.0

Fluorine binding site 3 out of 9 in 5gvm

Go back to Fluorine Binding Sites List in 5gvm
Fluorine binding site 3 out of 9 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS557


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Plasmodium Vivax Shmt Bound with Plp-Glycine and GS557 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:24.3
occ:1.00
 F46 A:G57502 0.0 24.3 1.0
C35 A:G57502 1.3 23.3 1.0
F48 A:G57502 2.0 23.2 1.0
F47 A:G57502 2.2 25.2 1.0
C18 A:G57502 2.3 23.4 1.0
C19 A:G57502 2.9 23.7 1.0
C17 A:G57502 3.4 22.9 1.0
CB A:CYS364 3.5 52.0 1.0
O A:CYS364 3.6 58.2 1.0
CG2 A:THR357 3.7 24.8 1.0
CB A:PRO367 3.7 33.9 1.0
CA A:CYS364 3.8 55.7 1.0
CG A:PRO367 3.9 34.6 1.0
SG A:CYS364 4.1 50.1 1.0
C A:CYS364 4.1 57.3 1.0
C20 A:G57502 4.2 23.4 1.0
CD A:PRO367 4.4 35.9 1.0
N A:THR357 4.5 23.8 1.0
C16 A:G57502 4.6 22.8 1.0
N9 A:G57502 4.7 24.4 1.0
CA A:PRO367 4.8 33.8 1.0
C21 A:G57502 4.9 23.4 1.0
C A:ASN356 4.9 22.3 1.0
CB A:THR357 4.9 24.9 1.0
N A:PRO367 5.0 37.3 1.0

Fluorine binding site 4 out of 9 in 5gvm

Go back to Fluorine Binding Sites List in 5gvm
Fluorine binding site 4 out of 9 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS557


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Plasmodium Vivax Shmt Bound with Plp-Glycine and GS557 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:25.1
occ:1.00
 F48 B:G57502 0.0 25.1 1.0
C35 B:G57502 1.3 25.1 1.0
F46 B:G57502 2.1 26.2 1.0
F47 B:G57502 2.2 26.6 1.0
C18 B:G57502 2.4 23.9 1.0
C17 B:G57502 2.8 22.9 1.0
O B:LYS355 3.2 22.9 1.0
C B:LYS355 3.4 23.4 1.0
N B:ASN356 3.5 23.0 1.0
CG B:PRO367 3.5 32.4 1.0
CB B:PRO367 3.6 32.0 1.0
CA B:ASN356 3.6 21.3 1.0
C19 B:G57502 3.6 23.1 1.0
C B:ASN356 4.0 22.2 1.0
CG B:LYS355 4.0 27.7 1.0
N B:THR357 4.0 23.1 1.0
CB B:LYS355 4.1 24.6 1.0
C16 B:G57502 4.2 22.4 1.0
N9 B:G57502 4.2 22.1 1.0
CD B:LYS355 4.2 28.5 1.0
CA B:LYS355 4.3 23.3 1.0
CG2 B:THR357 4.5 24.1 1.0
CD B:PRO367 4.6 32.8 1.0
C8 B:G57502 4.6 22.9 1.0
O B:ASN356 4.7 23.1 1.0
C20 B:G57502 4.8 22.5 1.0
C21 B:G57502 5.0 22.6 1.0

Fluorine binding site 5 out of 9 in 5gvm

Go back to Fluorine Binding Sites List in 5gvm
Fluorine binding site 5 out of 9 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS557


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Plasmodium Vivax Shmt Bound with Plp-Glycine and GS557 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:26.6
occ:1.00
 F47 B:G57502 0.0 26.6 1.0
C35 B:G57502 1.3 25.1 1.0
F46 B:G57502 2.2 26.2 1.0
F48 B:G57502 2.2 25.1 1.0
C18 B:G57502 2.3 23.9 1.0
C19 B:G57502 2.9 23.1 1.0
C17 B:G57502 3.4 22.9 1.0
NZ B:LYS355 3.4 31.8 1.0
CD B:LYS355 3.6 28.5 1.0
CE2 A:TYR63 3.8 24.2 1.0
CD2 A:TYR63 3.9 23.9 1.0
CG B:PRO367 3.9 32.4 1.0
O B:CYS364 4.1 51.9 1.0
CG B:LYS355 4.1 27.7 1.0
CE B:LYS355 4.1 30.9 1.0
C20 B:G57502 4.2 22.5 1.0
CD B:PRO367 4.4 32.8 1.0
CB B:PRO367 4.6 32.0 1.0
C16 B:G57502 4.6 22.4 1.0
CB B:LYS355 4.8 24.6 1.0
O B:LYS355 4.8 22.9 1.0
C21 B:G57502 4.9 22.6 1.0
CB B:CYS364 5.0 53.8 1.0

Fluorine binding site 6 out of 9 in 5gvm

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Fluorine binding site 6 out of 9 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS557


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Plasmodium Vivax Shmt Bound with Plp-Glycine and GS557 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:26.2
occ:1.00
 F46 B:G57502 0.0 26.2 1.0
C35 B:G57502 1.3 25.1 1.0
F48 B:G57502 2.1 25.1 1.0
F47 B:G57502 2.2 26.6 1.0
C18 B:G57502 2.3 23.9 1.0
C19 B:G57502 2.9 23.1 1.0
C17 B:G57502 3.3 22.9 1.0
CG2 B:THR357 3.6 24.1 1.0
CB B:CYS364 3.7 53.8 1.0
O B:CYS364 3.7 51.9 1.0
SG B:CYS364 3.8 54.5 1.0
CB B:PRO367 3.8 32.0 1.0
CG B:PRO367 3.9 32.4 1.0
CA B:CYS364 4.1 54.5 1.0
C20 B:G57502 4.2 22.5 1.0
CD B:PRO367 4.3 32.8 1.0
C B:CYS364 4.4 53.8 1.0
C16 B:G57502 4.5 22.4 1.0
N B:THR357 4.6 23.1 1.0
N9 B:G57502 4.6 22.1 1.0
C21 B:G57502 4.8 22.6 1.0
CA B:PRO367 4.9 32.1 1.0
CB B:THR357 4.9 24.4 1.0
N B:PRO367 5.0 33.9 1.0

Fluorine binding site 7 out of 9 in 5gvm

Go back to Fluorine Binding Sites List in 5gvm
Fluorine binding site 7 out of 9 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS557


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Plasmodium Vivax Shmt Bound with Plp-Glycine and GS557 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F502

b:24.2
occ:1.00
 F48 C:G57502 0.0 24.2 1.0
C35 C:G57502 1.3 24.1 1.0
F46 C:G57502 2.1 24.6 1.0
F47 C:G57502 2.2 25.7 1.0
C18 C:G57502 2.4 23.8 1.0
C17 C:G57502 2.8 22.7 1.0
O C:LYS355 3.1 24.2 1.0
C C:LYS355 3.3 23.0 1.0
N C:ASN356 3.4 22.1 1.0
CA C:ASN356 3.4 20.8 1.0
CG C:PRO367 3.5 33.5 1.0
CB C:PRO367 3.6 33.1 1.0
C19 C:G57502 3.7 23.4 1.0
C C:ASN356 3.8 21.3 1.0
N C:THR357 3.8 23.4 1.0
CG C:LYS355 3.9 26.3 1.0
CD C:LYS355 4.0 28.5 1.0
CB C:LYS355 4.0 23.7 1.0
N9 C:G57502 4.1 24.0 1.0
C16 C:G57502 4.2 22.7 1.0
CA C:LYS355 4.3 22.9 1.0
CG2 C:THR357 4.6 25.8 1.0
C8 C:G57502 4.6 23.5 1.0
CD C:PRO367 4.6 34.0 1.0
O C:ASN356 4.6 21.7 1.0
C20 C:G57502 4.8 23.6 1.0
CB C:ASN356 4.8 19.2 1.0
CA C:THR357 4.9 24.4 1.0
C21 C:G57502 5.0 23.5 1.0

Fluorine binding site 8 out of 9 in 5gvm

Go back to Fluorine Binding Sites List in 5gvm
Fluorine binding site 8 out of 9 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS557


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Plasmodium Vivax Shmt Bound with Plp-Glycine and GS557 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F502

b:25.7
occ:1.00
 F47 C:G57502 0.0 25.7 1.0
C35 C:G57502 1.3 24.1 1.0
F46 C:G57502 2.1 24.6 1.0
F48 C:G57502 2.2 24.2 1.0
C18 C:G57502 2.3 23.8 1.0
C19 C:G57502 2.9 23.4 1.0
CD C:LYS355 3.3 28.5 1.0
C17 C:G57502 3.4 22.7 1.0
NZ C:LYS355 3.4 31.6 1.0
CE C:LYS355 3.8 30.5 1.0
CG C:PRO367 3.8 33.5 1.0
CG C:LYS355 3.9 26.3 1.0
O C:CYS364 3.9 58.3 1.0
C20 C:G57502 4.2 23.6 1.0
CD C:PRO367 4.4 34.0 1.0
CB C:PRO367 4.5 33.1 1.0
C16 C:G57502 4.6 22.7 1.0
O C:LYS355 4.6 24.2 1.0
CB C:LYS355 4.6 23.7 1.0
C21 C:G57502 4.9 23.5 1.0
C C:LYS355 4.9 23.0 1.0
C C:CYS364 4.9 57.4 1.0
CB C:CYS364 5.0 54.5 1.0

Fluorine binding site 9 out of 9 in 5gvm

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Fluorine binding site 9 out of 9 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS557


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Plasmodium Vivax Shmt Bound with Plp-Glycine and GS557 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F502

b:24.6
occ:1.00
 F46 C:G57502 0.0 24.6 1.0
C35 C:G57502 1.3 24.1 1.0
F48 C:G57502 2.1 24.2 1.0
F47 C:G57502 2.1 25.7 1.0
C18 C:G57502 2.3 23.8 1.0
C19 C:G57502 2.9 23.4 1.0
C17 C:G57502 3.4 22.7 1.0
O C:CYS364 3.5 58.3 1.0
CB C:CYS364 3.6 54.5 1.0
CB C:PRO367 3.7 33.1 1.0
CG2 C:THR357 3.8 25.8 1.0
CA C:CYS364 3.8 56.8 1.0
CG C:PRO367 3.8 33.5 1.0
C C:CYS364 4.1 57.4 1.0
C20 C:G57502 4.2 23.6 1.0
CD C:PRO367 4.2 34.0 1.0
SG C:CYS364 4.5 53.5 1.0
N C:THR357 4.5 23.4 1.0
C16 C:G57502 4.6 22.7 1.0
N9 C:G57502 4.7 24.0 1.0
CA C:PRO367 4.8 33.1 1.0
C21 C:G57502 4.8 23.5 1.0
N C:PRO367 4.9 35.7 1.0
CD C:LYS355 4.9 28.5 1.0
CB C:THR357 5.0 25.5 1.0
C C:ASN356 5.0 21.3 1.0

Reference:

G.Schwertz, M.C.Witschel, M.Rottmann, R.Bonnert, U.Leartsakulpanich, P.Chitnumsub, A.Jaruwat, W.Ittarat, A.Schafer, R.A.Aponte, S.A.Charman, K.L.White, A.Kundu, S.Sadhukhan, M.Lloyd, G.M.Freiberg, M.Srikumaran, M.Siggel, A.Zwyssig, P.Chaiyen, F.Diederich. Antimalarial Inhibitors Targeting Serine Hydroxymethyltransferase (Shmt) with in Vivo Efficacy and Analysis of Their Binding Mode Based on X-Ray Cocrystal Structures J. Med. Chem. V. 60 4840 2017.
ISSN: ISSN 1520-4804
PubMed: 28537728
DOI: 10.1021/ACS.JMEDCHEM.7B00008
Page generated: Thu Aug 1 09:41:10 2024

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