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Fluorine in PDB 7eu5: Co-Crystal Structure of Human Nicotinamide N-Methyltransferase (Nnmt) with Tricyclic Small Molecule Inhibitor Jbsnf-000107

Enzymatic activity of Co-Crystal Structure of Human Nicotinamide N-Methyltransferase (Nnmt) with Tricyclic Small Molecule Inhibitor Jbsnf-000107

All present enzymatic activity of Co-Crystal Structure of Human Nicotinamide N-Methyltransferase (Nnmt) with Tricyclic Small Molecule Inhibitor Jbsnf-000107:
2.1.1.1;

Protein crystallography data

The structure of Co-Crystal Structure of Human Nicotinamide N-Methyltransferase (Nnmt) with Tricyclic Small Molecule Inhibitor Jbsnf-000107, PDB code: 7eu5 was solved by S.Swaminathan, R.Gosu, S.Birudukota, S.Kandan, K.Vaithilingam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.73 / 2.73
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 60.737, 62.543, 71.491, 94.21, 103, 103.65
R / Rfree (%) 20.8 / 28

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Co-Crystal Structure of Human Nicotinamide N-Methyltransferase (Nnmt) with Tricyclic Small Molecule Inhibitor Jbsnf-000107 (pdb code 7eu5). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Co-Crystal Structure of Human Nicotinamide N-Methyltransferase (Nnmt) with Tricyclic Small Molecule Inhibitor Jbsnf-000107, PDB code: 7eu5:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 7eu5

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Fluorine binding site 1 out of 4 in the Co-Crystal Structure of Human Nicotinamide N-Methyltransferase (Nnmt) with Tricyclic Small Molecule Inhibitor Jbsnf-000107


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 Human Nicotinamide N-Methyltransferase (Nnmt) with Tricyclic Small Molecule Inhibitor Jbsnf-000107 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F302

b:25.0
occ:1.00
 F11 A:JDL302 0.0 25.0 1.0
C10 A:JDL302 1.3 21.7 1.0
C9 A:JDL302 2.3 21.1 1.0
C12 A:JDL302 2.3 20.2 1.0
OG A:SER201 2.6 33.5 1.0
CB A:SER201 3.4 33.2 1.0
CB A:ASN249 3.5 27.1 1.0
C6 A:JDL302 3.5 19.1 1.0
CB A:ALA247 3.5 34.5 1.0
OD1 A:ASN249 3.6 22.7 1.0
CB A:ALA198 3.6 27.8 1.0
C13 A:JDL302 3.6 20.3 1.0
CG A:ASN249 3.7 26.4 1.0
O A:TYR203 3.8 24.8 1.0
C5 A:JDL302 4.0 19.3 1.0
N A:ASN249 4.2 29.0 1.0
CA A:ASN249 4.4 26.9 1.0
CD2 A:TYR242 4.4 26.8 1.0
N A:ASN248 4.5 30.3 1.0
ND2 A:ASN249 4.6 26.7 1.0
CA A:ALA247 4.6 34.3 1.0
CA A:SER201 4.7 31.9 1.0
CE2 A:TYR242 4.8 26.4 1.0
OG A:SER213 4.8 30.2 1.0
CB A:TYR204 4.8 27.5 1.0
C7 A:JDL302 4.8 19.3 1.0
C14 A:JDL302 4.9 19.8 1.0
C A:TYR203 4.9 28.2 1.0
C A:ALA247 5.0 33.5 1.0
OD1 A:ASN248 5.0 29.8 1.0

Fluorine binding site 2 out of 4 in 7eu5

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Fluorine binding site 2 out of 4 in the Co-Crystal Structure of Human Nicotinamide N-Methyltransferase (Nnmt) with Tricyclic Small Molecule Inhibitor Jbsnf-000107


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 Human Nicotinamide N-Methyltransferase (Nnmt) with Tricyclic Small Molecule Inhibitor Jbsnf-000107 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F302

b:19.5
occ:1.00
 F11 B:JDL302 0.0 19.5 1.0
C10 B:JDL302 1.3 20.3 1.0
C12 B:JDL302 2.2 22.1 1.0
C9 B:JDL302 2.3 20.1 1.0
OG B:SER201 3.1 27.2 1.0
CB B:ALA247 3.3 28.4 1.0
CB B:ASN249 3.5 23.3 1.0
OD1 B:ASN249 3.5 20.7 1.0
C13 B:JDL302 3.5 21.7 1.0
C6 B:JDL302 3.5 19.9 1.0
CB B:ALA198 3.6 24.4 1.0
CG B:ASN249 3.6 23.0 1.0
CB B:SER201 3.8 29.0 1.0
C5 B:JDL302 3.9 20.9 1.0
O B:TYR203 4.0 27.9 1.0
CD2 B:TYR242 4.3 23.6 1.0
N B:ASN249 4.3 23.3 1.0
CA B:ASN249 4.4 22.7 1.0
CA B:ALA247 4.5 27.5 1.0
ND2 B:ASN249 4.5 24.9 1.0
N B:ASN248 4.5 23.7 1.0
CE2 B:TYR242 4.6 22.2 1.0
CB B:TYR204 4.7 24.5 1.0
C14 B:JDL302 4.8 22.1 1.0
C B:ALA247 4.8 24.9 1.0
C7 B:JDL302 4.9 20.5 1.0
OG B:SER213 4.9 28.9 1.0

Fluorine binding site 3 out of 4 in 7eu5

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Fluorine binding site 3 out of 4 in the Co-Crystal Structure of Human Nicotinamide N-Methyltransferase (Nnmt) with Tricyclic Small Molecule Inhibitor Jbsnf-000107


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 Human Nicotinamide N-Methyltransferase (Nnmt) with Tricyclic Small Molecule Inhibitor Jbsnf-000107 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F302

b:26.6
occ:1.00
 F11 C:JDL302 0.0 26.6 1.0
C10 C:JDL302 1.3 24.8 1.0
C9 C:JDL302 2.3 25.2 1.0
C12 C:JDL302 2.3 24.8 1.0
OG C:SER201 2.7 36.2 1.0
CB C:ASN249 3.3 32.0 1.0
CB C:ALA247 3.4 41.7 1.0
C6 C:JDL302 3.6 25.0 1.0
C13 C:JDL302 3.6 24.9 1.0
CB C:SER201 3.6 36.3 1.0
CB C:ALA198 3.6 33.6 1.0
O C:TYR203 3.7 33.4 1.0
CG C:ASN249 3.8 30.2 1.0
C5 C:JDL302 4.0 24.7 1.0
OD1 C:ASN249 4.1 27.9 1.0
CA C:ASN249 4.3 32.4 1.0
N C:ASN249 4.5 33.9 1.0
CD2 C:TYR242 4.5 41.0 1.0
ND2 C:ASN249 4.5 30.7 1.0
CB C:TYR204 4.6 33.4 1.0
CA C:ALA247 4.6 39.0 1.0
C C:TYR203 4.7 32.6 1.0
OG C:SER213 4.8 32.0 1.0
CA C:SER201 4.8 34.8 1.0
C14 C:JDL302 4.9 24.3 1.0
C7 C:JDL302 4.9 24.5 1.0
CE2 C:TYR242 4.9 39.6 1.0

Fluorine binding site 4 out of 4 in 7eu5

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Fluorine binding site 4 out of 4 in the Co-Crystal Structure of Human Nicotinamide N-Methyltransferase (Nnmt) with Tricyclic Small Molecule Inhibitor Jbsnf-000107


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 Human Nicotinamide N-Methyltransferase (Nnmt) with Tricyclic Small Molecule Inhibitor Jbsnf-000107 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F302

b:29.7
occ:1.00
 F11 D:JDL302 0.0 29.7 1.0
C10 D:JDL302 1.4 31.0 1.0
C9 D:JDL302 2.4 31.2 1.0
C12 D:JDL302 2.4 32.0 1.0
OG D:SER201 3.0 32.5 1.0
CB D:ASN249 3.3 34.1 1.0
CB D:ALA247 3.4 35.3 1.0
CB D:SER201 3.5 32.1 1.0
CB D:ALA198 3.5 25.3 1.0
C6 D:JDL302 3.6 29.2 1.0
O D:TYR203 3.6 28.0 1.0
C13 D:JDL302 3.6 30.1 1.0
CG D:ASN249 3.8 33.1 1.0
C5 D:JDL302 4.0 28.3 1.0
OD1 D:ASN249 4.3 29.2 1.0
CA D:ASN249 4.3 34.2 1.0
ND2 D:ASN249 4.4 34.7 1.0
N D:ASN249 4.4 37.2 1.0
CD2 D:TYR242 4.5 29.2 1.0
CB D:TYR204 4.6 31.9 1.0
C D:TYR203 4.6 28.4 1.0
OG D:SER213 4.7 31.7 1.0
CA D:ALA247 4.7 36.7 1.0
CE2 D:TYR242 4.8 29.9 1.0
N D:ASN248 4.9 35.9 1.0
CA D:SER201 4.9 30.3 1.0
C7 D:JDL302 4.9 29.0 1.0
C14 D:JDL302 4.9 29.8 1.0
CA D:ALA198 5.0 24.7 1.0

Reference:

S.Ruf, S.Rajagopal, S.V.Kadnur, M.S.Hallur, S.Rani, R.Kristam, S.Swaminathan, B.R.Zope, P.K.Gondrala, I.Swamy, V.P.R.K.Putta, S.Kandan, G.Zech, H.Schreuder, C.Rudolph, R.Elvert, J.Czech, S.Birudukota, M.A.Siddiqui, N.N.Anand, V.S.Mane, S.Dittakavi, J.Suresh, R.Gosu, M.Ramesh, T.Yura, S.Dhakshinamoorthy, A.Kannt. Novel Tricyclic Small Molecule Inhibitors of Nicotinamide N-Methyltransferase For the Treatment of Metabolic Disorders. Sci Rep V. 12 15440 2022.
ISSN: ESSN 2045-2322
PubMed: 36104373
DOI: 10.1038/S41598-022-19634-2
Page generated: Fri Aug 2 06:45:37 2024

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