Fluorine in PDB 8pbo: Deep Interactome Learning For Generative Drug Design

The structure of Deep Interactome Learning For Generative Drug Design, PDB code: 8pbo was solved by M.Hakansson, D.Focht, K.Atz, G.Schneider, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.28 / 1.85
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	93.413, 60.611, 117.945, 90, 102.86, 90
R / Rfree (%)	17.1 / 21.3

The binding sites of Fluorine atom in the Deep Interactome Learning For Generative Drug Design (pdb code 8pbo). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Deep Interactome Learning For Generative Drug Design, PDB code: 8pbo:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Deep Interactome Learning For Generative Drug Design


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Deep Interactome Learning For Generative Drug Design within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:55.0 occ:1.00 F1 A:Y5I501 0.0 55.0 1.0 C18 A:Y5I501 1.4 42.2 1.0 C14 A:Y5I501 2.3 39.0 1.0 C19 A:Y5I501 2.4 45.5 1.0 H14 A:Y5I501 2.4 42.3 1.0 HE1 A:HIS449 2.5 37.5 1.0 H18 A:Y5I501 2.5 46.1 1.0 C15 A:Y5I501 2.8 42.6 1.0 HE2 A:LYS367 2.9 34.8 1.0 HD2 A:PHE363 2.9 47.5 1.0 CE1 A:HIS449 3.1 37.0 1.0 HE2 A:PHE363 3.2 47.2 1.0 HH A:TYR327 3.3 32.6 0.0 H17 A:Y5I501 3.4 44.0 1.0 C13 A:Y5I501 3.6 43.1 1.0 C11 A:Y5I501 3.6 51.0 1.0 ND1 A:HIS449 3.6 36.5 1.0 H15 A:Y5I501 3.6 41.8 1.0 HE1 A:TYR327 3.6 33.0 1.0 HD1 A:HIS449 3.6 30.2 0.0 CD2 A:PHE363 3.7 50.5 1.0 C16 A:Y5I501 3.7 44.1 1.0 CE A:LYS367 3.7 34.6 1.0 HB3 A:CYS285 3.8 35.4 1.0 HZ3 A:LYS367 3.8 38.1 1.0 CE2 A:PHE363 3.8 49.2 1.0 O A:HOH669 3.8 50.7 1.0 HE3 A:LYS367 3.9 34.6 1.0 NE2 A:HIS449 4.0 40.0 1.0 C12 A:Y5I501 4.1 47.2 1.0 NZ A:LYS367 4.1 39.3 1.0 OH A:TYR327 4.1 37.5 1.0 HG A:CYS285 4.1 33.5 0.0 HZ1 A:LYS367 4.2 38.2 1.0 H16 A:Y5I501 4.2 43.5 1.0 HE2 A:HIS449 4.2 33.4 0.0 HB2 A:CYS285 4.3 36.2 1.0 H13 A:Y5I501 4.3 43.0 1.0 CB A:CYS285 4.4 35.3 1.0 CE1 A:TYR327 4.4 31.8 1.0 SD A:MET364 4.6 48.8 1.0 HG2 A:LYS367 4.6 31.4 1.0 O2 A:Y5I501 4.7 47.6 1.0 CG A:HIS449 4.7 35.8 1.0 CZ A:TYR327 4.8 37.1 1.0 HE1 A:PHE282 4.8 44.6 1.0 O A:PHE363 4.8 37.4 1.0 HB2 A:PHE363 4.9 38.3 1.0 C17 A:Y5I501 4.9 43.1 1.0 O A:HOH605 4.9 52.9 1.0 CD A:LYS367 4.9 31.7 1.0 CD2 A:HIS449 4.9 38.3 1.0 CG A:PHE363 4.9 42.5 1.0 SG A:CYS285 5.0 39.4 1.0

Fluorine binding site 2 out of 2 in the Deep Interactome Learning For Generative Drug Design


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Deep Interactome Learning For Generative Drug Design within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:65.7 occ:1.00 F2 A:Y5I501 0.0 65.7 1.0 C20 A:Y5I501 1.4 48.8 1.0 C21 A:Y5I501 2.3 52.5 1.0 C7 A:Y5I501 2.4 42.0 1.0 H19 A:Y5I501 2.5 50.6 1.0 O1 A:Y5I501 2.7 45.2 1.0 O A:HOH691 2.9 47.5 1.0 HB2 A:ARG288 3.0 44.2 1.0 HA A:CYS285 3.1 35.2 1.0 HB3 A:ARG288 3.3 43.8 1.0 O A:GLY284 3.3 37.2 1.0 C A:GLY284 3.6 45.6 1.0 CB A:ARG288 3.6 42.2 1.0 O A:HOH654 3.6 61.9 1.0 C4 A:Y5I501 3.6 46.6 1.0 C6 A:Y5I501 3.6 48.9 1.0 H11 A:Y5I501 3.6 46.9 1.0 HG2 A:ARG288 3.7 53.7 1.0 N A:CYS285 3.8 37.4 1.0 CA A:CYS285 3.9 34.1 1.0 C5 A:Y5I501 4.1 44.5 1.0 C8 A:Y5I501 4.1 42.7 1.0 CG A:ARG288 4.2 55.3 1.0 HA3 A:GLY284 4.2 43.1 1.0 HB A:ILE341 4.2 36.1 1.0 H A:ARG288 4.3 38.3 1.0 HD2 A:ARG288 4.4 66.5 1.0 H A:CYS285 4.4 38.8 1.0 H5 A:Y5I501 4.4 46.0 1.0 HG22 A:ILE341 4.4 37.2 1.0 CA A:GLY284 4.4 43.3 1.0 C10 A:Y5I501 4.5 47.4 1.0 SG A:CYS285 4.5 39.4 1.0 H7 A:Y5I501 4.5 43.8 1.0 H6 A:Y5I501 4.6 43.9 1.0 H9 A:Y5I501 4.6 44.2 1.0 C9 A:Y5I501 4.7 44.0 1.0 H A:SER342 4.7 38.1 1.0 HG23 A:ILE341 4.7 38.0 1.0 O A:HOH651 4.7 45.0 1.0 HA2 A:GLY284 4.8 43.4 1.0 C3 A:Y5I501 4.8 58.8 1.0 H10 A:Y5I501 4.8 46.3 1.0 CB A:CYS285 4.8 35.3 1.0 CA A:ARG288 4.9 38.2 1.0 CD A:ARG288 4.9 66.2 1.0 C A:CYS285 4.9 38.4 1.0 CG2 A:ILE341 4.9 38.7 1.0 N A:ARG288 4.9 36.4 1.0 HG3 A:ARG288 5.0 53.5 1.0

K.Atz, L.Cotos, C.Isert, M.Hakansson, D.Focht, M.Hilleke, D.F.Nippa, M.Iff, J.Ledergerber, C.C.G.Schiebroek, V.Romeo, J.A.Hiss, D.Merk, P.Schneider, B.Kuhn, U.Grether, G.Schneider. Prospective De Novo Drug Design with Deep Interactome Learning. Nat Commun V. 15 3408 2024.
ISSN: ESSN 2041-1723
PubMed: 38649351
DOI: 10.1038/S41467-024-47613-W