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Fluorine in PDB 5nsd: Co-Crystal Structure of Nampt Dimer with Kpt-9274

Enzymatic activity of Co-Crystal Structure of Nampt Dimer with Kpt-9274

All present enzymatic activity of Co-Crystal Structure of Nampt Dimer with Kpt-9274:
2.4.2.12;

Protein crystallography data

The structure of Co-Crystal Structure of Nampt Dimer with Kpt-9274, PDB code: 5nsd was solved by J.E.Neggers, B.Kwanten, T.Dierckx, H.Noguchi, A.Voet, T.Vercruysse, E.Baloglu, W.Senapedis, M.Jacquemyn, D.Daelemans, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.20 / 2.05
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 62.138, 109.167, 84.974, 90.00, 96.63, 90.00
R / Rfree (%) 23.5 / 28.3

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Co-Crystal Structure of Nampt Dimer with Kpt-9274 (pdb code 5nsd). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Co-Crystal Structure of Nampt Dimer with Kpt-9274, PDB code: 5nsd:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 5nsd

Go back to Fluorine Binding Sites List in 5nsd
Fluorine binding site 1 out of 6 in the Co-Crystal Structure of Nampt Dimer with Kpt-9274


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Co-Crystal Structure of Nampt Dimer with Kpt-9274 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F511

b:61.9
occ:1.00
 F43 A:96Q511 0.0 61.9 1.0
C35 A:96Q511 1.4 58.2 1.0
F44 A:96Q511 2.2 65.9 1.0
C36 A:96Q511 2.3 58.0 1.0
C34 A:96Q511 2.3 49.2 1.0
O A:HOH842 3.0 37.7 1.0
C37 A:96Q511 3.0 54.0 1.0
C33 A:96Q511 3.4 49.2 1.0
N31 A:96Q511 3.4 49.9 1.0
C29 A:96Q511 4.6 41.7 1.0

Fluorine binding site 2 out of 6 in 5nsd

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Fluorine binding site 2 out of 6 in the Co-Crystal Structure of Nampt Dimer with Kpt-9274


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Co-Crystal Structure of Nampt Dimer with Kpt-9274 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F511

b:65.9
occ:1.00
 F44 A:96Q511 0.0 65.9 1.0
C35 A:96Q511 1.4 58.2 1.0
F43 A:96Q511 2.2 61.9 1.0
C34 A:96Q511 2.3 49.2 1.0
C36 A:96Q511 2.3 58.0 1.0
NE2 B:GLN92 3.5 45.0 1.0
C33 A:96Q511 3.5 49.2 1.0
C37 A:96Q511 3.7 54.0 1.0
N31 A:96Q511 4.2 49.9 1.0
CD B:GLN92 4.4 43.8 1.0
CE2 A:TYR240 4.5 35.1 1.0
CZ A:TYR240 4.6 40.5 1.0
O A:HOH842 4.6 37.7 1.0
OH A:TYR240 4.6 43.0 1.0
CG B:GLN92 4.8 38.2 1.0

Fluorine binding site 3 out of 6 in 5nsd

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Fluorine binding site 3 out of 6 in the Co-Crystal Structure of Nampt Dimer with Kpt-9274


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Co-Crystal Structure of Nampt Dimer with Kpt-9274 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F511

b:44.9
occ:1.00
 F45 A:96Q511 0.0 44.9 1.0
C40 A:96Q511 1.4 39.1 1.0
C41 A:96Q511 2.4 30.4 1.0
C39 A:96Q511 2.4 43.1 1.0
O A:HOH751 2.7 33.2 1.0
CB A:ARG349 3.0 19.1 1.0
CG A:ARG349 3.3 19.3 1.0
C42 A:96Q511 3.7 36.4 1.0
C38 A:96Q511 3.7 41.8 1.0
CD A:ARG349 3.8 27.0 1.0
O A:VAL350 4.1 19.9 1.0
O A:HOH878 4.1 35.2 1.0
C22 A:96Q511 4.2 40.0 1.0
N A:VAL350 4.3 21.2 1.0
CA A:ARG349 4.3 17.3 1.0
CB A:ALA379 4.4 21.4 1.0
N A:ALA379 4.6 18.7 1.0
CG2 A:ILE309 4.6 22.7 1.0
O A:ASN377 4.6 19.2 1.0
NE A:ARG349 4.6 31.1 1.0
CG1 A:ILE309 4.7 24.4 1.0
C A:ARG349 4.7 22.8 1.0
CD1 A:ILE309 4.7 25.0 1.0
C A:ILE378 4.8 16.8 1.0
C A:VAL350 4.8 21.6 1.0
O A:HOH969 4.9 40.4 1.0

Fluorine binding site 4 out of 6 in 5nsd

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Fluorine binding site 4 out of 6 in the Co-Crystal Structure of Nampt Dimer with Kpt-9274


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Co-Crystal Structure of Nampt Dimer with Kpt-9274 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F507

b:66.3
occ:1.00
 F43 B:96Q507 0.0 66.3 1.0
C35 B:96Q507 1.4 55.0 1.0
F44 B:96Q507 2.2 59.1 1.0
C36 B:96Q507 2.3 47.6 1.0
C34 B:96Q507 2.3 53.6 1.0
C37 B:96Q507 2.8 49.5 1.0
O B:HOH999 2.9 44.3 1.0
C33 B:96Q507 3.4 55.8 1.0
N31 B:96Q507 3.6 53.5 1.0
OE1 A:GLN92 4.0 50.8 1.0
O A:HOH760 4.6 41.6 1.0
CG A:GLN92 4.7 37.0 1.0
CD A:GLN92 4.7 46.9 1.0

Fluorine binding site 5 out of 6 in 5nsd

Go back to Fluorine Binding Sites List in 5nsd
Fluorine binding site 5 out of 6 in the Co-Crystal Structure of Nampt Dimer with Kpt-9274


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Co-Crystal Structure of Nampt Dimer with Kpt-9274 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F507

b:59.1
occ:1.00
 F44 B:96Q507 0.0 59.1 1.0
C35 B:96Q507 1.4 55.0 1.0
F43 B:96Q507 2.2 66.3 1.0
C36 B:96Q507 2.3 47.6 1.0
C34 B:96Q507 2.3 53.6 1.0
O A:HOH760 2.4 41.6 1.0
OE1 A:GLN92 2.6 50.8 1.0
CD A:GLN92 3.4 46.9 1.0
C33 B:96Q507 3.5 55.8 1.0
C37 B:96Q507 3.6 49.5 1.0
CG A:GLN92 4.0 37.0 1.0
N31 B:96Q507 4.2 53.5 1.0
NE2 A:GLN92 4.3 39.8 1.0
CE2 B:TYR240 4.4 37.2 1.0
CZ B:TYR240 4.6 38.2 1.0
OH B:TYR240 4.7 33.6 1.0
O B:HOH999 4.9 44.3 1.0
CD2 B:TYR240 4.9 40.4 1.0

Fluorine binding site 6 out of 6 in 5nsd

Go back to Fluorine Binding Sites List in 5nsd
Fluorine binding site 6 out of 6 in the Co-Crystal Structure of Nampt Dimer with Kpt-9274


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Co-Crystal Structure of Nampt Dimer with Kpt-9274 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F507

b:47.5
occ:1.00
 F45 B:96Q507 0.0 47.5 1.0
C40 B:96Q507 1.4 42.6 1.0
C41 B:96Q507 2.4 31.3 1.0
C39 B:96Q507 2.4 43.6 1.0
CB B:ARG349 3.0 23.2 1.0
CG B:ARG349 3.1 25.1 1.0
O B:HOH678 3.4 36.2 1.0
C42 B:96Q507 3.6 34.9 1.0
C38 B:96Q507 3.7 41.4 1.0
CD B:ARG349 3.8 28.2 1.0
O B:HOH965 4.1 31.1 1.0
C22 B:96Q507 4.1 43.7 1.0
CD1 B:ILE309 4.4 29.2 1.0
CG1 B:ILE309 4.4 24.6 1.0
CA B:ARG349 4.5 18.0 1.0
NE B:ARG349 4.5 25.7 1.0
CG2 B:ILE309 4.6 23.0 1.0
N B:VAL350 4.8 22.3 1.0
O B:VAL350 4.9 17.7 1.0

Reference:

J.E.Neggers, B.Kwanten, T.Dierckx, H.Noguchi, A.Voet, L.Bral, K.Minner, B.Massant, N.Kint, M.Delforge, T.Vercruysse, E.Baloglu, W.Senapedis, M.Jacquemyn, D.Daelemans. Target Identification of Small Molecules Using Large-Scale Crispr-Cas Mutagenesis Scanning of Essential Genes. Nat Commun V. 9 502 2018.
ISSN: ESSN 2041-1723
PubMed: 29402884
DOI: 10.1038/S41467-017-02349-8
Page generated: Tue Jul 15 05:32:40 2025

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