Fluorine in PDB 8og5: Crystal Structure of Human DCAF1 WD40 Repeats (Q1250L) in Complex with Compound 1

All present enzymatic activity of Crystal Structure of Human DCAF1 WD40 Repeats (Q1250L) in Complex with Compound 1:
2.7.11.1;

The structure of Crystal Structure of Human DCAF1 WD40 Repeats (Q1250L) in Complex with Compound 1, PDB code: 8og5 was solved by M.Schroeder, A.Vulpetti, M.Renatus, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	52.82 / 2.20
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	81.924, 81.924, 236.778, 90, 90, 120
R / Rfree (%)	19.7 / 23.5

The binding sites of Fluorine atom in the Crystal Structure of Human DCAF1 WD40 Repeats (Q1250L) in Complex with Compound 1 (pdb code 8og5). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of Human DCAF1 WD40 Repeats (Q1250L) in Complex with Compound 1, PDB code: 8og5:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of Human DCAF1 WD40 Repeats (Q1250L) in Complex with Compound 1


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 DCAF1 WD40 Repeats (Q1250L) in Complex with Compound 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1503 b:75.0 occ:1.00 F15 A:LQH1503 0.0 75.0 1.0 C10 A:LQH1503 1.3 68.3 1.0 HB2 A:HIS1140 2.3 38.8 1.0 C14 A:LQH1503 2.3 70.7 1.0 C5 A:LQH1503 2.4 65.0 1.0 HD1 A:TYR1181 2.7 40.9 1.0 C2 A:LQH1503 2.9 65.8 1.0 CB A:HIS1140 3.2 37.7 1.0 HB3 A:HIS1140 3.3 38.6 1.0 HE1 A:TYR1181 3.4 42.5 1.0 N1 A:LQH1503 3.4 63.8 1.0 CD1 A:TYR1181 3.5 42.1 1.0 HB A:THR1139 3.6 36.2 1.0 C19 A:LQH1503 3.6 82.2 1.0 C11 A:LQH1503 3.6 69.5 1.0 C4 A:LQH1503 3.7 61.0 1.0 C6 A:LQH1503 3.7 61.1 1.0 CG A:HIS1140 3.8 43.5 1.0 CE1 A:TYR1181 3.8 42.8 1.0 O A:THR1139 3.9 36.0 1.0 HD1 A:HIS1140 4.0 30.0 0.0 HG1 A:THR1139 4.0 30.0 0.0 OG1 A:THR1139 4.1 39.4 1.0 C16 A:LQH1503 4.1 78.7 1.0 ND1 A:HIS1140 4.1 48.6 1.0 C A:THR1139 4.2 35.9 1.0 CB A:THR1139 4.3 35.6 1.0 CA A:HIS1140 4.3 36.4 1.0 C3 A:LQH1503 4.4 58.1 1.0 HA A:HIS1140 4.4 36.3 1.0 N A:HIS1140 4.5 34.7 1.0 HB2 A:TYR1181 4.5 35.6 1.0 HB2 A:SER1153 4.6 32.9 1.0 CG A:TYR1181 4.7 36.6 1.0 C9 A:LQH1503 4.7 51.8 1.0 HA A:TYR1181 4.7 33.5 1.0 CD2 A:HIS1140 4.7 47.2 1.0 HB1 A:ALA1315 4.9 56.0 1.0 HG A:CYS1227 4.9 30.0 0.0 C12 A:LQH1503 4.9 64.1 1.0 CA A:THR1139 4.9 35.8 1.0 O A:HIS1180 5.0 36.8 1.0 O A:HOH1601 5.0 60.9 1.0 HB3 A:ALA1315 5.0 56.1 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of Human DCAF1 WD40 Repeats (Q1250L) in Complex with Compound 1


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 DCAF1 WD40 Repeats (Q1250L) in Complex with Compound 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1504 b:86.1 occ:1.00 F15 A:LQH1504 0.0 86.1 1.0 C10 A:LQH1504 1.3 96.6 1.0 C14 A:LQH1504 2.4 88.5 1.0 C5 A:LQH1504 2.4 108.2 1.0 C2 A:LQH1504 3.0 116.7 1.0 HB1 A:ALA1129 3.2 43.6 1.0 HB2 A:PHE1170 3.3 54.6 1.0 N1 A:LQH1504 3.6 117.3 1.0 C19 A:LQH1504 3.6 88.5 1.0 C11 A:LQH1504 3.7 97.1 1.0 C6 A:LQH1504 3.8 118.7 1.0 HD2 A:PHE1170 3.9 52.2 1.0 C4 A:LQH1504 3.9 107.3 1.0 HB2 A:TYR1131 4.0 39.1 1.0 HB3 A:PHE1170 4.0 54.4 1.0 CB A:ALA1129 4.0 43.6 1.0 CB A:PHE1170 4.0 55.4 1.0 HB3 A:ALA1129 4.1 43.5 1.0 C16 A:LQH1504 4.2 91.2 1.0 CD2 A:PHE1170 4.2 52.0 1.0 HB2 A:ALA1129 4.3 44.9 1.0 CG A:PHE1170 4.3 50.3 1.0 C3 A:LQH1504 4.5 123.3 1.0 H A:SER1130 4.5 41.9 1.0 O A:HOH1720 4.5 62.0 1.0 C9 A:LQH1504 4.6 108.8 1.0 HD1 A:TYR1131 4.7 43.1 1.0 O A:HOH1743 4.7 52.4 1.0 O A:SER1130 4.9 43.2 1.0 CB A:TYR1131 4.9 38.4 1.0 C12 A:LQH1504 5.0 127.2 1.0 N A:SER1130 5.0 41.6 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of Human DCAF1 WD40 Repeats (Q1250L) in Complex with Compound 1


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 DCAF1 WD40 Repeats (Q1250L) in Complex with Compound 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1505 b:58.2 occ:0.50 F15 A:LQH1505 0.0 58.2 0.5 C10 A:LQH1505 1.3 57.0 0.5 O A:ARG1283 1.9 67.0 1.0 C4 A:LQH1505 2.1 57.7 0.5 C5 A:LQH1505 2.3 59.0 0.5 C14 A:LQH1505 2.4 55.8 0.5 N1 A:LQH1505 2.6 62.1 0.5 C2 A:LQH1505 2.8 60.8 0.5 C A:ARG1283 3.0 59.6 1.0 HA A:ARG1283 3.1 64.2 1.0 O A:HOH1740 3.2 50.9 1.0 C9 A:LQH1505 3.5 58.0 0.5 C11 A:LQH1505 3.6 58.0 0.5 CA A:ARG1283 3.6 63.7 1.0 C19 A:LQH1505 3.6 53.3 0.5 C3 A:LQH1505 3.7 62.9 0.5 O A:LEU1282 3.8 56.5 1.0 C6 A:LQH1505 4.0 58.5 0.5 C16 A:LQH1505 4.1 55.9 0.5 N A:THR1284 4.1 54.7 1.0 HA A:THR1284 4.1 55.0 1.0 N8 A:LQH1505 4.2 60.5 0.5 HB3 A:ARG1283 4.5 72.9 1.0 HZ A:PHE1285 4.6 35.4 0.5 N A:ARG1283 4.6 61.2 1.0 C A:LEU1282 4.6 57.2 1.0 CA A:THR1284 4.6 54.1 1.0 CB A:ARG1283 4.7 72.2 1.0 CZ A:PHE1285 4.7 34.9 0.5 HG3 A:ARG1283 4.7 78.2 1.0 CE2 A:PHE1285 4.8 36.4 0.5 HE2 A:PHE1285 4.8 37.2 0.5 H A:THR1284 4.9 54.8 1.0 C7 A:LQH1505 4.9 63.1 0.5 C12 A:LQH1505 5.0 60.8 0.5

A.Vulpetti, P.Holzer, N.Schmiedeberg, P.Imbach-Weese, C.Pissot-Soldermann, G.J.Hollingworth, T.Radimerski, C.R.Thoma, T.M.Stachyra, M.Wojtynek, M.Maschlej, S.Chau, A.Schuffenhauer, C.Fernandez, M.Schroder, M.Renatus. Discovery of New Binders For DCAF1, An Emerging Ligase Target in the Targeted Protein Degradation Field Acs Med.Chem.Lett. 2023.
ISSN: ISSN 1948-5875
DOI: 10.1021/ACSMEDCHEMLETT.3C00104