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Fluorine in PDB 5gvp: Plasmodium Vivax Shmt Bound with Plp-Glycine and GS654

Protein crystallography data

The structure of Plasmodium Vivax Shmt Bound with Plp-Glycine and GS654, PDB code: 5gvp 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 / 2.26
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 102.075, 58.928, 234.830, 90.00, 90.06, 90.00
R / Rfree (%) 25 / 31.2

Other elements in 5gvp:

The structure of Plasmodium Vivax Shmt Bound with Plp-Glycine and GS654 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 GS654 (pdb code 5gvp). 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 GS654, PDB code: 5gvp:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Fluorine binding site 1 out of 9 in 5gvp

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Fluorine binding site 1 out of 9 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS654


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 GS654 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:27.9
occ:1.00
 F48 A:GCF502 0.0 27.9 1.0
C35 A:GCF502 1.3 29.1 1.0
F46 A:GCF502 2.2 31.9 1.0
F47 A:GCF502 2.2 29.2 1.0
C18 A:GCF502 2.4 26.4 1.0
C17 A:GCF502 2.8 25.4 1.0
O A:LYS355 3.5 25.8 1.0
CG A:PRO367 3.6 37.2 1.0
CB A:PRO367 3.6 37.1 1.0
C19 A:GCF502 3.7 25.6 1.0
C A:LYS355 3.7 25.1 1.0
CA A:ASN356 3.8 24.2 1.0
N A:ASN356 3.8 24.8 1.0
CD A:LYS355 4.0 31.2 1.0
N A:THR357 4.1 26.1 1.0
CG A:LYS355 4.1 29.1 1.0
C16 A:GCF502 4.2 24.3 1.0
N9 A:GCF502 4.2 26.6 1.0
C A:ASN356 4.2 24.9 1.0
CB A:LYS355 4.4 26.2 1.0
CD A:PRO367 4.4 38.1 1.0
CG2 A:THR357 4.5 29.9 1.0
CA A:LYS355 4.7 24.8 1.0
C8 A:GCF502 4.7 26.6 1.0
C20 A:GCF502 4.8 25.0 1.0
SG A:CYS364 4.8 59.1 1.0
CE A:LYS355 4.8 32.4 1.0

Fluorine binding site 2 out of 9 in 5gvp

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Fluorine binding site 2 out of 9 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS654


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 GS654 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:29.2
occ:1.00
 F47 A:GCF502 0.0 29.2 1.0
C35 A:GCF502 1.3 29.1 1.0
F46 A:GCF502 2.1 31.9 1.0
F48 A:GCF502 2.2 27.9 1.0
C18 A:GCF502 2.3 26.4 1.0
C19 A:GCF502 2.9 25.6 1.0
CD A:LYS355 3.4 31.2 1.0
NZ A:LYS355 3.4 34.2 1.0
C17 A:GCF502 3.4 25.4 1.0
CE A:LYS355 3.6 32.4 1.0
CE2 B:TYR63 4.0 20.9 1.0
CD2 B:TYR63 4.1 22.1 1.0
CG A:LYS355 4.1 29.1 1.0
CG A:PRO367 4.1 37.2 1.0
C20 A:GCF502 4.2 25.0 1.0
CD A:PRO367 4.5 38.1 1.0
C16 A:GCF502 4.6 24.3 1.0
CB A:PRO367 4.8 37.1 1.0
O A:CYS364 4.8 63.7 1.0
SG A:CYS364 4.9 59.1 1.0
C21 A:GCF502 4.9 25.1 1.0
O A:LYS355 4.9 25.8 1.0
CB A:LYS355 5.0 26.2 1.0

Fluorine binding site 3 out of 9 in 5gvp

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Fluorine binding site 3 out of 9 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS654


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 GS654 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:31.9
occ:1.00
 F46 A:GCF502 0.0 31.9 1.0
C35 A:GCF502 1.3 29.1 1.0
F47 A:GCF502 2.1 29.2 1.0
F48 A:GCF502 2.2 27.9 1.0
C18 A:GCF502 2.3 26.4 1.0
C19 A:GCF502 2.9 25.6 1.0
SG A:CYS364 2.9 59.1 1.0
C17 A:GCF502 3.4 25.4 1.0
O A:CYS364 3.5 63.7 1.0
CG2 A:THR357 4.0 29.9 1.0
CG A:PRO367 4.1 37.2 1.0
CD A:PRO367 4.1 38.1 1.0
C20 A:GCF502 4.2 25.0 1.0
CB A:PRO367 4.2 37.1 1.0
CB A:CYS364 4.4 59.6 1.0
C A:CYS364 4.5 61.7 1.0
C16 A:GCF502 4.6 24.3 1.0
CA A:CYS364 4.7 60.4 1.0
N9 A:GCF502 4.8 26.6 1.0
C21 A:GCF502 4.9 25.1 1.0
N A:PRO367 5.0 39.9 1.0

Fluorine binding site 4 out of 9 in 5gvp

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Fluorine binding site 4 out of 9 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS654


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 GS654 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F503

b:28.2
occ:1.00
 F48 A:GCF503 0.0 28.2 1.0
C35 A:GCF503 1.3 29.0 1.0
F46 A:GCF503 2.2 31.1 1.0
F47 A:GCF503 2.2 28.3 1.0
C18 A:GCF503 2.4 26.1 1.0
C17 A:GCF503 2.8 25.3 1.0
CG B:PRO367 3.4 37.9 1.0
O B:LYS355 3.5 26.5 1.0
CB B:PRO367 3.6 37.9 1.0
C19 A:GCF503 3.7 25.2 1.0
C B:LYS355 3.7 25.7 1.0
N B:ASN356 3.8 24.9 1.0
CA B:ASN356 3.9 24.2 1.0
CD B:LYS355 4.0 32.5 1.0
N B:THR357 4.1 26.6 1.0
CG B:LYS355 4.2 30.9 1.0
N9 A:GCF503 4.2 24.8 1.0
C16 A:GCF503 4.2 24.5 1.0
C B:ASN356 4.2 25.4 1.0
CD B:PRO367 4.2 38.3 1.0
CB B:LYS355 4.3 28.1 1.0
CG2 B:THR357 4.6 28.5 1.0
CA B:LYS355 4.7 25.8 1.0
C8 A:GCF503 4.7 24.8 1.0
C20 A:GCF503 4.8 24.7 1.0
SG B:CYS364 4.8 56.8 1.0
O B:CYS364 5.0 64.7 1.0
CA B:PRO367 5.0 38.1 1.0

Fluorine binding site 5 out of 9 in 5gvp

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Fluorine binding site 5 out of 9 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS654


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 GS654 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F503

b:28.3
occ:1.00
 F47 A:GCF503 0.0 28.3 1.0
C35 A:GCF503 1.3 29.0 1.0
F48 A:GCF503 2.2 28.2 1.0
F46 A:GCF503 2.2 31.1 1.0
C18 A:GCF503 2.3 26.1 1.0
C19 A:GCF503 2.9 25.2 1.0
C17 A:GCF503 3.5 25.3 1.0
NZ B:LYS355 3.5 34.8 1.0
CD B:LYS355 3.5 32.5 1.0
CE B:LYS355 4.1 34.1 1.0
CG B:PRO367 4.1 37.9 1.0
CE2 A:TYR63 4.1 21.4 1.0
O B:CYS364 4.1 64.7 1.0
C20 A:GCF503 4.2 24.7 1.0
CD2 A:TYR63 4.2 23.1 1.0
CG B:LYS355 4.3 30.9 1.0
CD B:PRO367 4.3 38.3 1.0
C16 A:GCF503 4.6 24.5 1.0
CB B:PRO367 4.8 37.9 1.0
C21 A:GCF503 4.9 24.9 1.0
SG B:CYS364 5.0 56.8 1.0
CB B:LYS355 5.0 28.1 1.0

Fluorine binding site 6 out of 9 in 5gvp

Go back to Fluorine Binding Sites List in 5gvp
Fluorine binding site 6 out of 9 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS654


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 GS654 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F503

b:31.1
occ:1.00
 F46 A:GCF503 0.0 31.1 1.0
C35 A:GCF503 1.3 29.0 1.0
F48 A:GCF503 2.2 28.2 1.0
F47 A:GCF503 2.2 28.3 1.0
C18 A:GCF503 2.3 26.1 1.0
C19 A:GCF503 2.9 25.2 1.0
SG B:CYS364 3.0 56.8 1.0
O B:CYS364 3.1 64.7 1.0
C17 A:GCF503 3.3 25.3 1.0
CB B:CYS364 3.8 57.1 1.0
C B:CYS364 4.0 62.3 1.0
CG2 B:THR357 4.0 28.5 1.0
CG B:PRO367 4.1 37.9 1.0
CA B:CYS364 4.1 59.6 1.0
CD B:PRO367 4.1 38.3 1.0
C20 A:GCF503 4.2 24.7 1.0
CB B:PRO367 4.2 37.9 1.0
C16 A:GCF503 4.5 24.5 1.0
N9 A:GCF503 4.7 24.8 1.0
C21 A:GCF503 4.8 24.9 1.0
N B:THR357 4.9 26.6 1.0
N B:PRO367 5.0 40.3 1.0

Fluorine binding site 7 out of 9 in 5gvp

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Fluorine binding site 7 out of 9 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS654


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 GS654 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F502

b:29.2
occ:1.00
 F48 C:GCF502 0.0 29.2 1.0
C35 C:GCF502 1.3 30.4 1.0
F46 C:GCF502 2.1 33.4 1.0
F47 C:GCF502 2.2 30.4 1.0
C18 C:GCF502 2.4 28.4 1.0
C17 C:GCF502 2.8 27.3 1.0
O C:LYS355 3.5 24.6 1.0
CG C:PRO367 3.6 37.2 1.0
C19 C:GCF502 3.6 27.7 1.0
C C:LYS355 3.7 24.3 1.0
CB C:PRO367 3.7 37.6 1.0
CG C:LYS355 3.8 29.2 1.0
N C:ASN356 3.8 24.4 1.0
CA C:ASN356 3.9 22.8 1.0
CD C:LYS355 4.0 31.5 1.0
N C:THR357 4.2 26.3 1.0
CB C:LYS355 4.2 26.6 1.0
C16 C:GCF502 4.2 26.0 1.0
C C:ASN356 4.3 24.4 1.0
N9 C:GCF502 4.3 25.2 1.0
CD C:PRO367 4.4 37.6 1.0
CG2 C:THR357 4.6 30.1 1.0
CA C:LYS355 4.6 24.1 1.0
C8 C:GCF502 4.8 25.4 1.0
C20 C:GCF502 4.8 26.7 1.0
SG C:CYS364 4.8 64.3 1.0
C21 C:GCF502 5.0 27.1 1.0

Fluorine binding site 8 out of 9 in 5gvp

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Fluorine binding site 8 out of 9 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS654


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 GS654 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F502

b:30.4
occ:1.00
 F47 C:GCF502 0.0 30.4 1.0
C35 C:GCF502 1.3 30.4 1.0
F46 C:GCF502 2.1 33.4 1.0
F48 C:GCF502 2.2 29.2 1.0
C18 C:GCF502 2.3 28.4 1.0
C19 C:GCF502 2.9 27.7 1.0
CD C:LYS355 3.4 31.5 1.0
C17 C:GCF502 3.4 27.3 1.0
NZ C:LYS355 3.6 34.4 1.0
CG C:LYS355 3.9 29.2 1.0
CE C:LYS355 3.9 32.9 1.0
CG C:PRO367 4.1 37.2 1.0
C20 C:GCF502 4.2 26.7 1.0
O C:CYS364 4.5 63.5 1.0
CD C:PRO367 4.5 37.6 1.0
C16 C:GCF502 4.6 26.0 1.0
CB C:LYS355 4.9 26.6 1.0
SG C:CYS364 4.9 64.3 1.0
C21 C:GCF502 4.9 27.1 1.0
CB C:PRO367 4.9 37.6 1.0

Fluorine binding site 9 out of 9 in 5gvp

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Fluorine binding site 9 out of 9 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS654


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 GS654 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F502

b:33.4
occ:1.00
 F46 C:GCF502 0.0 33.4 1.0
C35 C:GCF502 1.3 30.4 1.0
F47 C:GCF502 2.1 30.4 1.0
F48 C:GCF502 2.1 29.2 1.0
C18 C:GCF502 2.3 28.4 1.0
C19 C:GCF502 2.9 27.7 1.0
SG C:CYS364 3.0 64.3 1.0
O C:CYS364 3.3 63.5 1.0
C17 C:GCF502 3.4 27.3 1.0
CG C:PRO367 3.9 37.2 1.0
CG2 C:THR357 4.0 30.1 1.0
CD C:PRO367 4.0 37.6 1.0
CB C:CYS364 4.1 62.9 1.0
CB C:PRO367 4.2 37.6 1.0
C20 C:GCF502 4.2 26.7 1.0
C C:CYS364 4.2 63.0 1.0
CA C:CYS364 4.4 63.5 1.0
C16 C:GCF502 4.6 26.0 1.0
N9 C:GCF502 4.9 25.2 1.0
C21 C:GCF502 4.9 27.1 1.0
N C:PRO367 5.0 39.6 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 09:41:40 2024

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