Fluorine in PDB 3nj4: Fluoro-Neplanocin A in Human S-Adenosylhomocysteine Hydrolase

All present enzymatic activity of Fluoro-Neplanocin A in Human S-Adenosylhomocysteine Hydrolase:
3.3.1.1;

The structure of Fluoro-Neplanocin A in Human S-Adenosylhomocysteine Hydrolase, PDB code: 3nj4 was solved by L.S.Jeong, K.M.Lee, K.Y.Hwang, S.Choi, Y.S.Heo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.61 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	91.201, 81.939, 129.599, 90.00, 107.01, 90.00
R / Rfree (%)	20.7 / 26.1

The binding sites of Fluorine atom in the Fluoro-Neplanocin A in Human S-Adenosylhomocysteine Hydrolase (pdb code 3nj4). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Fluoro-Neplanocin A in Human S-Adenosylhomocysteine Hydrolase, PDB code: 3nj4:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Fluoro-Neplanocin A in Human S-Adenosylhomocysteine Hydrolase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Fluoro-Neplanocin A in Human S-Adenosylhomocysteine Hydrolase within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:36.4 occ:1.00 F1 A:AFX601 0.0 36.4 1.0 C5' A:AFX601 1.4 32.5 1.0 C4' A:AFX601 2.4 31.8 1.0 C1' A:AFX601 2.5 33.1 1.0 NE2 A:HIS55 2.7 40.8 1.0 C1 A:AFX601 2.9 31.3 1.0 CD2 A:HIS55 3.0 40.2 1.0 O1 A:AFX601 3.0 27.5 1.0 CD1 A:LEU347 3.1 23.1 1.0 N9 A:AFX601 3.1 33.0 1.0 CE1 A:HIS55 3.3 39.3 1.0 CD1 A:LEU344 3.6 23.9 1.0 CG A:HIS55 3.6 40.5 1.0 C3' A:AFX601 3.6 32.5 1.0 C2' A:AFX601 3.8 32.7 1.0 ND1 A:HIS55 3.8 40.1 1.0 C4 A:AFX601 3.8 33.7 1.0 C8 A:AFX601 3.8 31.7 1.0 O7N A:NAD501 4.3 32.2 1.0 C7N A:NAD501 4.3 31.2 1.0 N3 A:AFX601 4.3 33.7 1.0 OD2 A:ASP131 4.4 41.2 1.0 N7N A:NAD501 4.4 31.4 1.0 CG A:LEU347 4.4 25.0 1.0 CB A:HIS55 4.7 39.0 1.0 C5 A:AFX601 4.7 34.7 1.0 O3' A:AFX601 4.8 33.7 1.0 OD1 A:ASP131 4.8 39.6 1.0 N7 A:AFX601 4.8 32.9 1.0 O2' A:AFX601 4.9 34.6 1.0 CG A:ASP131 4.9 40.5 1.0 C3N A:NAD501 5.0 29.8 1.0

Fluorine binding site 2 out of 4 in the Fluoro-Neplanocin A in Human S-Adenosylhomocysteine Hydrolase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Fluoro-Neplanocin A in Human S-Adenosylhomocysteine Hydrolase within 5.0Å range: probe atom residue distance (Å) B Occ B:F602 b:35.0 occ:1.00 F1 B:AFX602 0.0 35.0 1.0 C5' B:AFX602 1.4 32.7 1.0 C4' B:AFX602 2.4 33.4 1.0 C1' B:AFX602 2.5 32.3 1.0 NE2 B:HIS55 2.6 17.3 1.0 CD2 B:HIS55 2.9 19.0 1.0 C1 B:AFX602 2.9 34.2 1.0 N9 B:AFX602 3.0 32.5 1.0 O1 B:AFX602 3.0 34.9 1.0 CD1 B:LEU347 3.0 20.7 1.0 CE1 B:HIS55 3.5 15.5 1.0 C3' B:AFX602 3.6 33.5 1.0 C8 B:AFX602 3.7 31.5 1.0 C4 B:AFX602 3.7 31.2 1.0 C2' B:AFX602 3.7 32.6 1.0 CD1 B:LEU344 3.7 19.4 1.0 CG B:HIS55 3.8 21.6 1.0 ND1 B:HIS55 4.1 19.8 1.0 OD2 B:ASP131 4.2 37.7 1.0 O7N B:NAD502 4.3 33.5 1.0 N3 B:AFX602 4.3 26.8 1.0 C7N B:NAD502 4.3 32.2 1.0 CG B:LEU347 4.3 23.3 1.0 N7N B:NAD502 4.6 29.4 1.0 C5 B:AFX602 4.7 32.4 1.0 N7 B:AFX602 4.7 33.0 1.0 O3' B:AFX602 4.7 35.7 1.0 C3N B:NAD502 4.8 32.7 1.0 O2' B:AFX602 4.8 32.8 1.0 OD1 B:ASP131 4.9 35.7 1.0 CG B:ASP131 4.9 36.5 1.0 CB B:HIS55 5.0 21.1 1.0

Fluorine binding site 3 out of 4 in the Fluoro-Neplanocin A in Human S-Adenosylhomocysteine Hydrolase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Fluoro-Neplanocin A in Human S-Adenosylhomocysteine Hydrolase within 5.0Å range: probe atom residue distance (Å) B Occ C:F603 b:37.0 occ:1.00 F1 C:AFX603 0.0 37.0 1.0 C5' C:AFX603 1.4 35.4 1.0 C4' C:AFX603 2.4 35.2 1.0 C1' C:AFX603 2.5 35.7 1.0 NE2 C:HIS55 2.7 36.5 1.0 O1 C:AFX603 2.9 37.2 1.0 C1 C:AFX603 3.0 35.5 1.0 CD2 C:HIS55 3.0 37.4 1.0 N9 C:AFX603 3.1 34.5 1.0 CD1 C:LEU347 3.2 36.8 1.0 CE1 C:HIS55 3.5 36.8 1.0 C3' C:AFX603 3.6 34.1 1.0 C2' C:AFX603 3.8 34.5 1.0 C8 C:AFX603 3.8 34.0 1.0 CD1 C:LEU344 3.8 34.2 1.0 CG C:HIS55 3.9 38.1 1.0 C4 C:AFX603 3.9 33.3 1.0 OD2 C:ASP131 3.9 49.2 1.0 ND1 C:HIS55 4.1 37.5 1.0 O7N C:NAD503 4.4 30.6 1.0 C7N C:NAD503 4.4 31.2 1.0 N3 C:AFX603 4.5 32.8 1.0 CG C:LEU347 4.6 34.9 1.0 N7N C:NAD503 4.6 29.4 1.0 O3' C:AFX603 4.8 33.8 1.0 CG C:ASP131 4.8 48.6 1.0 C5 C:AFX603 4.8 33.7 1.0 N7 C:AFX603 4.8 34.0 1.0 O2' C:AFX603 4.8 38.2 1.0 C3N C:NAD503 4.9 30.1 1.0 OD1 C:ASP131 4.9 47.1 1.0 CB C:HIS55 5.0 39.5 1.0

Fluorine binding site 4 out of 4 in the Fluoro-Neplanocin A in Human S-Adenosylhomocysteine Hydrolase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Fluoro-Neplanocin A in Human S-Adenosylhomocysteine Hydrolase within 5.0Å range: probe atom residue distance (Å) B Occ D:F604 b:32.7 occ:1.00 F1 D:AFX604 0.0 32.7 1.0 C5' D:AFX604 1.4 29.9 1.0 C4' D:AFX604 2.4 29.4 1.0 C1' D:AFX604 2.5 30.4 1.0 NE2 D:HIS55 2.7 18.8 1.0 O1 D:AFX604 2.9 31.8 1.0 C1 D:AFX604 3.0 30.4 1.0 CD2 D:HIS55 3.0 21.8 1.0 N9 D:AFX604 3.0 29.4 1.0 CD1 D:LEU347 3.2 28.6 1.0 C3' D:AFX604 3.6 29.7 1.0 CE1 D:HIS55 3.7 22.2 1.0 C8 D:AFX604 3.7 30.5 1.0 C2' D:AFX604 3.7 28.4 1.0 CD1 D:LEU344 3.7 20.1 1.0 C4 D:AFX604 3.8 30.2 1.0 OD2 D:ASP131 4.0 46.2 1.0 CG D:HIS55 4.0 23.6 1.0 C7N D:NAD504 4.2 31.7 1.0 O7N D:NAD504 4.2 30.6 1.0 ND1 D:HIS55 4.3 22.1 1.0 N3 D:AFX604 4.4 29.2 1.0 N7N D:NAD504 4.4 32.1 1.0 CG D:LEU347 4.6 28.6 1.0 C3N D:NAD504 4.6 30.8 1.0 C5 D:AFX604 4.7 30.7 1.0 N7 D:AFX604 4.7 32.0 1.0 O3' D:AFX604 4.7 32.6 1.0 O2' D:AFX604 4.8 33.1 1.0 CG D:ASP131 4.9 43.8 1.0 OD1 D:ASP131 4.9 42.5 1.0

K.M.Lee, W.J.Choi, Y.Lee, H.J.Lee, L.X.Zhao, H.W.Lee, J.G.Park, H.O.Kim, K.Y.Hwang, Y.S.Heo, S.Choi, L.S.Jeong. X-Ray Crystal Structure and Binding Mode Analysis of Human S-Adenosylhomocysteine Hydrolase Complexed with Novel Mechanism-Based Inhibitors, Haloneplanocin A Analogues. J.Med.Chem. V. 54 930 2011.
ISSN: ISSN 0022-2623
PubMed: 21226494
DOI: 10.1021/JM1010836