Chlorine in PDB 8ood: Crystal Structure of Human DCAF1 WD40 Repeats (Q1250L) in Complex with Compound 15

All present enzymatic activity of Crystal Structure of Human DCAF1 WD40 Repeats (Q1250L) in Complex with Compound 15:
2.7.11.1;

The structure of Crystal Structure of Human DCAF1 WD40 Repeats (Q1250L) in Complex with Compound 15, PDB code: 8ood was solved by M.Schroeder, M.Renatus, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	52.26 / 1.50
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	81.496, 81.496, 232.723, 90, 90, 120
R / Rfree (%)	17 / 18.6

The structure of Crystal Structure of Human DCAF1 WD40 Repeats (Q1250L) in Complex with Compound 15 also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Chlorine atom in the Crystal Structure of Human DCAF1 WD40 Repeats (Q1250L) in Complex with Compound 15 (pdb code 8ood). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Crystal Structure of Human DCAF1 WD40 Repeats (Q1250L) in Complex with Compound 15, PDB code: 8ood:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Crystal Structure of Human DCAF1 WD40 Repeats (Q1250L) in Complex with Compound 15


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Human DCAF1 WD40 Repeats (Q1250L) in Complex with Compound 15 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1509 b:17.2 occ:1.00 CL55 A:VY31509 0.0 17.2 1.0 C16 A:VY31509 1.8 14.8 1.0 C17 A:VY31509 2.7 16.0 1.0 C15 A:VY31509 2.7 15.3 1.0 HD22 A:LEU1313 3.0 15.6 1.0 HB2 A:ARG1298 3.0 14.9 0.5 HB2 A:ARG1298 3.1 19.4 0.5 H11 A:EDO1504 3.1 19.8 1.0 HD13 A:ILE1262 3.1 14.3 1.0 HB3 A:ARG1225 3.2 14.2 1.0 HD12 A:ILE1262 3.4 14.6 1.0 HE1 A:PHE1330 3.4 16.6 1.0 HD11 A:ILE1262 3.4 14.2 1.0 HD2 A:ARG1298 3.4 15.1 0.5 HG3 A:ARG1225 3.4 16.8 1.0 HG3 A:ARG1298 3.5 22.7 0.5 CD1 A:ILE1262 3.5 14.9 1.0 HD12 A:LEU1313 3.6 15.9 1.0 HO1 A:EDO1504 3.6 38.0 0.0 HB2 A:ARG1225 3.7 14.6 1.0 CB A:ARG1225 3.8 13.9 1.0 CD2 A:LEU1313 3.8 16.3 1.0 C1 A:EDO1504 3.8 21.1 1.0 H12 A:EDO1504 3.8 19.8 1.0 CB A:ARG1298 3.9 19.1 0.5 CB A:ARG1298 3.9 14.6 0.5 HG A:LEU1313 3.9 15.8 1.0 C18 A:VY31509 4.0 14.7 1.0 C14 A:VY31509 4.0 14.5 1.0 CG A:ARG1298 4.0 22.7 0.5 HD23 A:LEU1313 4.0 15.9 1.0 CG A:ARG1225 4.1 17.0 1.0 HD3 A:ARG1298 4.1 27.2 0.5 O1 A:EDO1504 4.1 15.3 1.0 HA A:ARG1298 4.1 14.9 0.5 HA A:ARG1298 4.2 17.1 0.5 HD2 A:ARG1298 4.2 26.9 0.5 HD2 A:ARG1225 4.2 18.9 1.0 HG3 A:ARG1298 4.2 15.0 0.5 CE1 A:PHE1330 4.2 16.4 1.0 CG A:LEU1313 4.2 15.6 1.0 CD A:ARG1298 4.3 15.6 0.5 HZ A:PHE1330 4.3 17.3 1.0 CD1 A:LEU1313 4.3 16.6 1.0 CG A:ARG1298 4.3 15.2 0.5 CD A:ARG1298 4.4 27.6 0.5 CA A:ARG1298 4.4 17.2 0.5 CA A:ARG1298 4.4 15.0 0.5 C13 A:VY31509 4.5 13.5 1.0 H A:ARG1298 4.5 15.7 0.5 HD21 A:LEU1313 4.6 16.2 1.0 N A:ARG1298 4.6 15.4 0.5 HB3 A:ARG1298 4.6 15.1 0.5 HB3 A:ARG1298 4.6 19.5 0.5 CD A:ARG1225 4.6 18.9 1.0 N A:ARG1298 4.6 16.6 0.5 CZ A:PHE1330 4.7 17.7 1.0 H A:ARG1298 4.7 16.9 0.5 HA A:ILE1262 4.8 12.7 1.0 HD3 A:ARG1298 4.8 15.2 0.5 HG2 A:ARG1225 4.9 17.1 1.0 HD11 A:LEU1313 4.9 16.5 1.0 HG2 A:ARG1298 4.9 22.8 0.5 O A:ARG1225 4.9 13.3 1.0 HD13 A:LEU1313 5.0 16.5 1.0 CG1 A:ILE1262 5.0 13.8 1.0

Chlorine binding site 2 out of 3 in the Crystal Structure of Human DCAF1 WD40 Repeats (Q1250L) in Complex with Compound 15


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Human DCAF1 WD40 Repeats (Q1250L) in Complex with Compound 15 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1510 b:20.2 occ:0.50 CL55 A:VY31510 0.0 20.2 0.5 CL55 A:VY31510 0.9 32.6 0.5 C16 A:VY31510 1.7 21.1 0.5 C16 A:VY31510 1.9 26.9 0.5 C17 A:VY31510 2.5 27.6 0.5 HD23 A:LEU1117 2.5 16.9 0.5 C17 A:VY31510 2.6 21.9 0.5 HA A:SER1130 2.7 15.5 0.5 C15 A:VY31510 2.7 23.9 0.5 O A:LEU1117 2.8 14.5 0.5 HG A:LEU1117 3.0 16.2 0.5 C15 A:VY31510 3.1 27.2 0.5 O A:LEU1117 3.1 14.2 0.5 CA A:SER1130 3.3 15.8 0.5 HA A:SER1130 3.3 15.3 0.5 CD2 A:LEU1117 3.3 16.6 0.5 HA A:LYS1118 3.3 15.7 1.0 C A:SER1130 3.4 15.0 0.5 HB2 A:TYR1131 3.4 14.7 1.0 H A:TYR1131 3.4 14.2 1.0 HB3 A:LEU1117 3.5 14.9 0.5 CG A:LEU1117 3.5 15.9 0.5 C A:LEU1117 3.5 13.8 0.5 N A:SER1130 3.5 16.7 0.5 N A:TYR1131 3.5 14.7 1.0 C A:LEU1117 3.6 14.2 0.5 HD22 A:LEU1117 3.6 16.6 0.5 HB3 A:ALA1129 3.7 18.3 1.0 HB3 A:LEU1117 3.7 13.5 0.5 C A:SER1130 3.7 15.2 0.5 CA A:SER1130 3.7 15.7 0.5 N A:SER1130 3.8 16.6 0.5 HB3 A:TYR1131 3.8 13.9 1.0 C18 A:VY31510 3.8 29.4 0.5 C A:ALA1129 3.9 17.8 1.0 H A:SER1130 3.9 17.2 0.5 O A:ALA1129 3.9 17.0 1.0 O A:SER1130 3.9 14.4 0.5 C18 A:VY31510 3.9 24.8 0.5 HE1 A:MET1109 3.9 31.3 0.5 CB A:LEU1117 3.9 14.6 0.5 HB1 A:ALA1129 4.0 18.6 1.0 H A:LEU1119 4.0 16.6 1.0 N A:LYS1118 4.0 14.4 1.0 CB A:TYR1131 4.0 14.5 1.0 C14 A:VY31510 4.0 24.8 0.5 CA A:LYS1118 4.0 14.9 1.0 HD21 A:LEU1117 4.1 16.3 0.5 C14 A:VY31510 4.2 29.9 0.5 H A:SER1130 4.2 17.1 0.5 CB A:ALA1129 4.2 18.8 1.0 HB2 A:LEU1119 4.3 19.9 1.0 HB2 A:LEU1117 4.3 13.4 0.5 N A:LEU1119 4.3 16.1 1.0 C A:LYS1118 4.3 15.8 1.0 CB A:LEU1117 4.3 13.3 0.5 CA A:TYR1131 4.4 14.1 1.0 CA A:LEU1117 4.4 13.6 0.5 C13 A:VY31510 4.5 27.7 0.5 C13 A:VY31510 4.5 31.2 0.5 CA A:LEU1117 4.5 13.1 0.5 O A:SER1130 4.5 15.4 0.5 HE2 A:PHE1170 4.6 21.3 1.0 CB A:SER1130 4.6 16.8 0.5 H A:LYS1118 4.7 14.0 1.0 CE2 A:PHE1170 4.7 23.1 1.0 CA A:ALA1129 4.7 18.4 1.0 CE A:MET1109 4.8 31.2 0.5 HD2 A:PHE1170 4.8 21.8 1.0 HB2 A:LEU1117 4.8 14.3 0.5 HB2 A:SER1130 4.8 16.6 0.5 SD A:MET1109 4.9 31.8 0.5 CD1 A:LEU1117 4.9 16.4 0.5 CD2 A:PHE1170 4.9 21.6 1.0 H A:LEU1117 4.9 13.0 0.5 H A:LEU1117 4.9 13.3 0.5 HB3 A:SER1130 5.0 17.1 0.5

Chlorine binding site 3 out of 3 in the Crystal Structure of Human DCAF1 WD40 Repeats (Q1250L) in Complex with Compound 15


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Human DCAF1 WD40 Repeats (Q1250L) in Complex with Compound 15 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1510 b:32.6 occ:0.50 CL55 A:VY31510 0.0 32.6 0.5 CL55 A:VY31510 0.9 20.2 0.5 HD23 A:LEU1117 1.7 16.9 0.5 C16 A:VY31510 1.7 26.9 0.5 C16 A:VY31510 1.8 21.1 0.5 CD2 A:LEU1117 2.5 16.6 0.5 C15 A:VY31510 2.5 23.9 0.5 HG A:LEU1117 2.5 16.2 0.5 C17 A:VY31510 2.6 27.6 0.5 C15 A:VY31510 2.7 27.2 0.5 HD22 A:LEU1117 2.8 16.6 0.5 C17 A:VY31510 2.9 21.9 0.5 CG A:LEU1117 2.9 15.9 0.5 O A:LEU1117 3.1 14.5 0.5 HB3 A:LEU1117 3.1 14.9 0.5 HB3 A:LEU1117 3.2 13.5 0.5 HE1 A:MET1109 3.2 31.3 0.5 HD21 A:LEU1117 3.3 16.3 0.5 O A:LEU1117 3.4 14.2 0.5 HA A:SER1130 3.4 15.5 0.5 HB2 A:TYR1131 3.5 14.7 1.0 CB A:LEU1117 3.5 14.6 0.5 C A:LEU1117 3.6 13.8 0.5 C A:LEU1117 3.7 14.2 0.5 HB3 A:TYR1131 3.7 13.9 1.0 HE2 A:PHE1170 3.8 21.3 1.0 HB2 A:LEU1117 3.8 13.4 0.5 C14 A:VY31510 3.8 24.8 0.5 HA A:LYS1118 3.8 15.7 1.0 H A:TYR1131 3.8 14.2 1.0 CB A:LEU1117 3.9 13.3 0.5 C18 A:VY31510 3.9 29.4 0.5 C14 A:VY31510 3.9 29.9 0.5 CE2 A:PHE1170 4.0 23.1 1.0 N A:TYR1131 4.0 14.7 1.0 CB A:TYR1131 4.0 14.5 1.0 C A:SER1130 4.0 15.0 0.5 C18 A:VY31510 4.1 24.8 0.5 HA A:SER1130 4.1 15.3 0.5 CA A:SER1130 4.1 15.8 0.5 CE A:MET1109 4.1 31.2 0.5 N A:LYS1118 4.1 14.4 1.0 CA A:LEU1117 4.2 13.6 0.5 HD2 A:PHE1170 4.3 21.8 1.0 HB3 A:ALA1129 4.3 18.3 1.0 CD1 A:LEU1117 4.3 16.4 0.5 CD2 A:PHE1170 4.3 21.6 1.0 CA A:LEU1117 4.3 13.1 0.5 HB2 A:LEU1117 4.3 14.3 0.5 CA A:LYS1118 4.3 14.9 1.0 N A:SER1130 4.4 16.7 0.5 C A:SER1130 4.4 15.2 0.5 HB2 A:LEU1119 4.4 19.9 1.0 HD12 A:LEU1117 4.4 16.2 0.5 SD A:MET1109 4.4 31.8 0.5 C13 A:VY31510 4.4 31.2 0.5 C13 A:VY31510 4.4 27.7 0.5 H A:LEU1119 4.5 16.6 1.0 O A:SER1130 4.5 14.4 0.5 C A:LYS1118 4.5 15.8 1.0 CA A:SER1130 4.6 15.7 0.5 CZ A:PHE1170 4.6 19.1 1.0 HB1 A:ALA1129 4.6 18.6 1.0 HE2 A:MET1109 4.6 31.2 0.5 HE3 A:MET1109 4.6 20.1 0.5 N A:SER1130 4.6 16.6 0.5 N A:LEU1119 4.6 16.1 1.0 CA A:TYR1131 4.7 14.1 1.0 O A:ALA1129 4.7 17.0 1.0 HE2 A:MET1109 4.7 19.4 0.5 H A:LYS1118 4.7 14.0 1.0 HE3 A:MET1109 4.7 30.8 0.5 H A:SER1130 4.7 17.2 0.5 C A:ALA1129 4.7 17.8 1.0 HD11 A:LEU1117 4.8 16.0 0.5 HZ A:PHE1170 4.8 19.3 1.0 H A:LEU1117 4.9 13.0 0.5 CB A:ALA1129 4.9 18.8 1.0 HD13 A:LEU1117 4.9 15.8 0.5 H A:LEU1117 4.9 13.3 0.5 HA A:LEU1117 4.9 13.4 0.5

M.Schroder, M.Renatus, C.R.Thoma. Reinstating Targeted Protein Degradation with DCAF1 Protacs in Crbn Protac Resistant Settings Biorxiv 2023.
ISSN: ISSN 2692-8205
DOI: 10.1101/2023.04.09.536153