Fluorine in PDB 8im2: Crystal Structure of Human Hppd Complexed with Ntbc

All present enzymatic activity of Crystal Structure of Human Hppd Complexed with Ntbc:
1.13.11.27;

The structure of Crystal Structure of Human Hppd Complexed with Ntbc, PDB code: 8im2 was solved by J.Dong, H.-Y.Lin, G.-F.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.67 / 2.81
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	121.55, 147.442, 133.93, 90, 97.12, 90
R / Rfree (%)	21.3 / 25.4

The structure of Crystal Structure of Human Hppd Complexed with Ntbc also contains other interesting chemical elements:

Cobalt

(Co)

6 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Fluorine atom in the Crystal Structure of Human Hppd Complexed with Ntbc (pdb code 8im2). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 18 binding sites of Fluorine where determined in the Crystal Structure of Human Hppd Complexed with Ntbc, PDB code: 8im2:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 18 in the Crystal Structure of Human Hppd Complexed with Ntbc


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Human Hppd Complexed with Ntbc within 5.0Å range: probe atom residue distance (Å) B Occ A:F402 b:52.8 occ:1.00 F2 A:NTD402 0.0 52.8 1.0 C14 A:NTD402 1.4 51.7 1.0 F3 A:NTD402 2.2 49.9 1.0 F1 A:NTD402 2.2 57.4 1.0 C11 A:NTD402 2.4 50.2 1.0 C12 A:NTD402 2.9 45.0 1.0 CB A:ASN363 3.3 52.2 1.0 C10 A:NTD402 3.4 50.9 1.0 CD1 A:LEU323 3.6 36.9 1.0 CD1 A:LEU367 3.7 54.1 1.0 CE2 A:PHE336 3.9 44.2 1.0 OE1 A:GLN334 4.0 45.2 1.0 CG A:ASN363 4.1 48.6 1.0 C13 A:NTD402 4.2 43.3 1.0 ND2 A:ASN363 4.4 47.2 1.0 C A:ASN363 4.4 54.6 1.0 CA A:ASN363 4.4 53.8 1.0 O A:GLY360 4.5 51.2 1.0 C9 A:NTD402 4.6 47.3 1.0 CD2 A:PHE336 4.6 42.9 1.0 CZ A:PHE336 4.6 45.2 1.0 O A:ASN363 4.6 52.7 1.0 N A:PHE364 4.8 58.3 1.0 CG A:LEU367 4.8 52.8 1.0 CD A:GLN334 4.9 44.8 1.0 OD1 A:ASN363 4.9 47.4 1.0 C8 A:NTD402 4.9 44.0 1.0 CG A:LEU323 5.0 44.0 1.0

Fluorine binding site 2 out of 18 in the Crystal Structure of Human Hppd Complexed with Ntbc


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Human Hppd Complexed with Ntbc within 5.0Å range: probe atom residue distance (Å) B Occ A:F402 b:49.9 occ:1.00 F3 A:NTD402 0.0 49.9 1.0 C14 A:NTD402 1.4 51.7 1.0 F2 A:NTD402 2.2 52.8 1.0 F1 A:NTD402 2.2 57.4 1.0 C11 A:NTD402 2.4 50.2 1.0 C10 A:NTD402 2.7 50.9 1.0 CD1 A:LEU367 3.6 54.1 1.0 C12 A:NTD402 3.7 45.0 1.0 CE1 A:PHE364 4.0 55.2 1.0 C9 A:NTD402 4.1 47.3 1.0 CD1 A:PHE364 4.3 57.6 1.0 CZ A:PHE364 4.4 50.6 1.0 CE2 A:PHE336 4.7 44.2 1.0 C13 A:NTD402 4.8 43.3 1.0 N A:NTD402 4.9 52.0 1.0 C8 A:NTD402 4.9 44.0 1.0 CG A:PHE364 5.0 54.2 1.0

Fluorine binding site 3 out of 18 in the Crystal Structure of Human Hppd Complexed with Ntbc


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Human Hppd Complexed with Ntbc within 5.0Å range: probe atom residue distance (Å) B Occ A:F402 b:57.4 occ:1.00 F1 A:NTD402 0.0 57.4 1.0 C14 A:NTD402 1.4 51.7 1.0 F3 A:NTD402 2.2 49.9 1.0 F2 A:NTD402 2.2 52.8 1.0 C11 A:NTD402 2.4 50.2 1.0 C12 A:NTD402 3.0 45.0 1.0 N A:PHE364 3.2 58.3 1.0 CD1 A:PHE364 3.3 57.6 1.0 CG A:PHE364 3.4 54.2 1.0 C10 A:NTD402 3.4 50.9 1.0 C A:ASN363 3.4 54.6 1.0 CE1 A:PHE364 3.5 55.2 1.0 CB A:ASN363 3.6 52.2 1.0 CD2 A:PHE364 3.6 54.2 1.0 CA A:PHE364 3.6 57.9 1.0 CZ A:PHE364 3.7 50.6 1.0 CE2 A:PHE364 3.7 53.2 1.0 O A:ASN363 3.9 52.7 1.0 CA A:ASN363 4.0 53.8 1.0 CB A:PHE364 4.0 57.8 1.0 CD1 A:LEU367 4.0 54.1 1.0 O A:GLY360 4.1 51.2 1.0 C13 A:NTD402 4.3 43.3 1.0 C9 A:NTD402 4.6 47.3 1.0 N A:ASN363 4.6 57.3 1.0 CG A:ASN363 4.9 48.6 1.0 C8 A:NTD402 4.9 44.0 1.0

Fluorine binding site 4 out of 18 in the Crystal Structure of Human Hppd Complexed with Ntbc


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Human Hppd Complexed with Ntbc within 5.0Å range: probe atom residue distance (Å) B Occ B:F502 b:71.1 occ:1.00 F2 B:NTD502 0.0 71.1 1.0 C14 B:NTD502 1.4 67.2 1.0 F3 B:NTD502 2.2 62.6 1.0 F1 B:NTD502 2.2 67.1 1.0 C11 B:NTD502 2.4 59.6 1.0 C12 B:NTD502 3.1 59.2 1.0 C10 B:NTD502 3.3 57.7 1.0 CD1 B:PHE364 3.3 63.0 1.0 N B:PHE364 3.4 69.6 1.0 CE1 B:PHE364 3.4 63.2 1.0 CG B:PHE364 3.5 68.2 1.0 CB B:ASN363 3.5 66.9 1.0 CZ B:PHE364 3.6 62.4 1.0 C B:ASN363 3.6 67.5 1.0 CD2 B:PHE364 3.6 66.9 1.0 CE2 B:PHE364 3.7 62.8 1.0 CA B:PHE364 3.9 68.8 1.0 O B:GLY360 3.9 65.0 1.0 O B:ASN363 4.1 65.7 1.0 CA B:ASN363 4.1 67.8 1.0 CB B:PHE364 4.3 68.2 1.0 C13 B:NTD502 4.3 59.5 1.0 C9 B:NTD502 4.5 58.8 1.0 CD1 B:LEU367 4.6 63.7 1.0 N B:ASN363 4.7 67.5 1.0 CG B:ASN363 4.9 57.9 1.0 C8 B:NTD502 4.9 58.2 1.0

Fluorine binding site 5 out of 18 in the Crystal Structure of Human Hppd Complexed with Ntbc


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Human Hppd Complexed with Ntbc within 5.0Å range: probe atom residue distance (Å) B Occ B:F502 b:62.6 occ:1.00 F3 B:NTD502 0.0 62.6 1.0 C14 B:NTD502 1.4 67.2 1.0 F2 B:NTD502 2.2 71.1 1.0 F1 B:NTD502 2.2 67.1 1.0 C11 B:NTD502 2.4 59.6 1.0 C12 B:NTD502 2.9 59.2 1.0 CB B:ASN363 3.3 66.9 1.0 C10 B:NTD502 3.5 57.7 1.0 CD1 B:LEU323 3.8 55.4 1.0 CD1 B:LEU367 3.8 63.7 1.0 CE2 B:PHE336 3.9 50.6 1.0 CG B:ASN363 4.1 57.9 1.0 C13 B:NTD502 4.2 59.5 1.0 OE1 B:GLN334 4.2 56.8 1.0 O B:GLY360 4.4 65.0 1.0 ND2 B:ASN363 4.4 59.8 1.0 CD2 B:PHE336 4.5 52.4 1.0 CA B:ASN363 4.6 67.8 1.0 C B:ASN363 4.6 67.5 1.0 C9 B:NTD502 4.7 58.8 1.0 CZ B:PHE336 4.8 58.2 1.0 O B:ASN363 4.8 65.7 1.0 OD1 B:ASN363 4.9 57.8 1.0 C8 B:NTD502 4.9 58.2 1.0 N B:PHE364 4.9 69.6 1.0

Fluorine binding site 6 out of 18 in the Crystal Structure of Human Hppd Complexed with Ntbc


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Human Hppd Complexed with Ntbc within 5.0Å range: probe atom residue distance (Å) B Occ B:F502 b:67.1 occ:1.00 F1 B:NTD502 0.0 67.1 1.0 C14 B:NTD502 1.4 67.2 1.0 F2 B:NTD502 2.2 71.1 1.0 F3 B:NTD502 2.2 62.6 1.0 C11 B:NTD502 2.4 59.6 1.0 C10 B:NTD502 2.7 57.7 1.0 C12 B:NTD502 3.6 59.2 1.0 CE1 B:PHE364 4.0 63.2 1.0 C9 B:NTD502 4.1 58.8 1.0 C1 B:MPD503 4.2 69.0 1.0 CD1 B:LEU367 4.3 63.7 1.0 CM B:MPD503 4.3 69.0 1.0 CD1 B:PHE364 4.4 63.0 1.0 CZ B:PHE364 4.4 62.4 1.0 CE2 B:PHE336 4.6 50.6 1.0 C5 B:MPD503 4.7 64.2 1.0 C13 B:NTD502 4.8 59.5 1.0 CD2 B:PHE336 4.9 52.4 1.0 C2 B:MPD503 4.9 74.6 1.0 C8 B:NTD502 4.9 58.2 1.0 N B:NTD502 5.0 63.8 1.0

Fluorine binding site 7 out of 18 in the Crystal Structure of Human Hppd Complexed with Ntbc


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of Human Hppd Complexed with Ntbc within 5.0Å range: probe atom residue distance (Å) B Occ C:F402 b:60.2 occ:1.00 F2 C:NTD402 0.0 60.2 1.0 C14 C:NTD402 1.4 51.0 1.0 F1 C:NTD402 2.2 44.5 1.0 F3 C:NTD402 2.2 54.7 1.0 C11 C:NTD402 2.4 48.0 1.0 C12 C:NTD402 3.0 46.5 1.0 CD1 C:PHE364 3.1 55.0 1.0 CE1 C:PHE364 3.2 54.0 1.0 CG C:PHE364 3.3 57.5 1.0 N C:PHE364 3.3 64.1 1.0 C10 C:NTD402 3.4 50.2 1.0 CZ C:PHE364 3.5 54.4 1.0 CD2 C:PHE364 3.5 57.7 1.0 C C:ASN363 3.6 60.5 1.0 CA C:PHE364 3.6 60.9 1.0 CB C:ASN363 3.6 53.5 1.0 CE2 C:PHE364 3.7 55.9 1.0 CD1 C:LEU367 3.7 52.5 1.0 CB C:PHE364 4.0 60.0 1.0 O C:ASN363 4.0 60.5 1.0 CA C:ASN363 4.1 56.8 1.0 O C:GLY360 4.2 55.6 1.0 C13 C:NTD402 4.3 49.0 1.0 C9 C:NTD402 4.6 49.4 1.0 N C:ASN363 4.7 59.9 1.0 CG C:LEU367 4.8 55.4 1.0 C8 C:NTD402 4.9 50.7 1.0

Fluorine binding site 8 out of 18 in the Crystal Structure of Human Hppd Complexed with Ntbc


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of Human Hppd Complexed with Ntbc within 5.0Å range: probe atom residue distance (Å) B Occ C:F402 b:54.7 occ:1.00 F3 C:NTD402 0.0 54.7 1.0 C14 C:NTD402 1.4 51.0 1.0 F1 C:NTD402 2.2 44.5 1.0 F2 C:NTD402 2.2 60.2 1.0 C11 C:NTD402 2.4 48.0 1.0 C12 C:NTD402 2.9 46.5 1.0 CB C:ASN363 3.2 53.5 1.0 CD1 C:LEU367 3.4 52.5 1.0 CD1 C:LEU323 3.4 46.1 1.0 C10 C:NTD402 3.5 50.2 1.0 OE1 C:GLN334 3.6 52.3 1.0 CE2 C:PHE336 3.7 45.3 1.0 CG C:ASN363 4.0 55.0 1.0 C13 C:NTD402 4.2 49.0 1.0 C C:ASN363 4.4 60.5 1.0 CA C:ASN363 4.4 56.8 1.0 O C:GLY360 4.4 55.6 1.0 OD1 C:ASN363 4.4 54.6 1.0 CG C:LEU367 4.4 55.4 1.0 CZ C:PHE336 4.5 43.8 1.0 CD C:GLN334 4.5 47.4 1.0 CD2 C:PHE336 4.5 48.5 1.0 O C:ASN363 4.6 60.5 1.0 C9 C:NTD402 4.6 49.4 1.0 N C:PHE364 4.7 64.1 1.0 CG C:LEU323 4.8 50.7 1.0 ND2 C:ASN363 4.9 53.2 1.0 C8 C:NTD402 4.9 50.7 1.0

Fluorine binding site 9 out of 18 in the Crystal Structure of Human Hppd Complexed with Ntbc


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Crystal Structure of Human Hppd Complexed with Ntbc within 5.0Å range: probe atom residue distance (Å) B Occ C:F402 b:44.5 occ:1.00 F1 C:NTD402 0.0 44.5 1.0 C14 C:NTD402 1.4 51.0 1.0 F3 C:NTD402 2.2 54.7 1.0 F2 C:NTD402 2.2 60.2 1.0 C11 C:NTD402 2.4 48.0 1.0 C10 C:NTD402 2.7 50.2 1.0 CD1 C:LEU367 3.3 52.5 1.0 C12 C:NTD402 3.7 46.5 1.0 CE1 C:PHE364 3.9 54.0 1.0 C9 C:NTD402 4.0 49.4 1.0 CE2 C:PHE336 4.2 45.3 1.0 CD1 C:PHE364 4.2 55.0 1.0 CZ C:PHE364 4.5 54.4 1.0 CD2 C:PHE336 4.7 48.5 1.0 C13 C:NTD402 4.8 49.0 1.0 CG C:LEU367 4.8 55.4 1.0 CD1 C:LEU323 4.9 46.1 1.0 N C:NTD402 4.9 50.0 1.0 C8 C:NTD402 4.9 50.7 1.0 C4 C:MPD403 4.9 65.5 1.0 CZ C:PHE336 4.9 43.8 1.0 CG C:PHE364 5.0 57.5 1.0 CM C:MPD403 5.0 60.3 1.0

Fluorine binding site 10 out of 18 in the Crystal Structure of Human Hppd Complexed with Ntbc


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Crystal Structure of Human Hppd Complexed with Ntbc within 5.0Å range: probe atom residue distance (Å) B Occ D:F403 b:61.7 occ:1.00 F2 D:NTD403 0.0 61.7 1.0 C14 D:NTD403 1.4 56.1 1.0 F1 D:NTD403 2.2 51.3 1.0 F3 D:NTD403 2.2 54.6 1.0 C11 D:NTD403 2.4 54.0 1.0 C12 D:NTD403 2.9 47.6 1.0 CD1 D:PHE364 3.1 51.8 1.0 N D:PHE364 3.1 56.7 1.0 CG D:PHE364 3.3 58.6 1.0 CE1 D:PHE364 3.3 51.0 1.0 C D:ASN363 3.4 58.7 1.0 C10 D:NTD403 3.5 53.0 1.0 CB D:ASN363 3.5 51.1 1.0 CA D:PHE364 3.5 57.6 1.0 CD2 D:PHE364 3.6 60.3 1.0 CZ D:PHE364 3.6 55.2 1.0 CE2 D:PHE364 3.8 53.3 1.0 O D:ASN363 3.8 59.8 1.0 CB D:PHE364 4.0 60.3 1.0 O D:GLY360 4.0 56.3 1.0 CA D:ASN363 4.0 57.3 1.0 C13 D:NTD403 4.2 49.9 1.0 CD1 D:LEU367 4.3 55.4 1.0 N D:ASN363 4.6 57.5 1.0 C9 D:NTD403 4.6 53.6 1.0 CG D:ASN363 4.9 51.4 1.0 C D:PHE364 4.9 65.9 1.0 C8 D:NTD403 4.9 51.2 1.0

J.Dong, H.Xiao, J.N.Chen, B.F.Zheng, Y.L.Xu, M.X.Chen, W.C.Yang, H.Y.Lin, G.F.Yang. Structure-Based Discovery of Pyrazole-Benzothiadiazole Hybrid As Human Hppd Inhibitors. Structure 2023.
ISSN: ISSN 0969-2126
PubMed: 37794595
DOI: 10.1016/J.STR.2023.09.005