Fluorine in PDB 6bg3: Structure of (3S,4S)-1-Benzyl-4-(3-(3-(Trifluoromethyl)Phenyl)Ureido) Piperidin-3-Yl Acetate Bound to DCN1

All present enzymatic activity of Structure of (3S,4S)-1-Benzyl-4-(3-(3-(Trifluoromethyl)Phenyl)Ureido) Piperidin-3-Yl Acetate Bound to DCN1:
3.2.1.17;

The structure of Structure of (3S,4S)-1-Benzyl-4-(3-(3-(Trifluoromethyl)Phenyl)Ureido) Piperidin-3-Yl Acetate Bound to DCN1, PDB code: 6bg3 was solved by R.K.Guy, B.A.Schulman, D.C.Scott, J.T.Hammill, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.28 / 1.05
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	35.169, 96.915, 59.388, 90.00, 105.50, 90.00
R / Rfree (%)	15.6 / 17.4

The binding sites of Fluorine atom in the Structure of (3S,4S)-1-Benzyl-4-(3-(3-(Trifluoromethyl)Phenyl)Ureido) Piperidin-3-Yl Acetate Bound to DCN1 (pdb code 6bg3). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Structure of (3S,4S)-1-Benzyl-4-(3-(3-(Trifluoromethyl)Phenyl)Ureido) Piperidin-3-Yl Acetate Bound to DCN1, PDB code: 6bg3:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Structure of (3S,4S)-1-Benzyl-4-(3-(3-(Trifluoromethyl)Phenyl)Ureido) Piperidin-3-Yl Acetate Bound to DCN1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of (3S,4S)-1-Benzyl-4-(3-(3-(Trifluoromethyl)Phenyl)Ureido) Piperidin-3-Yl Acetate Bound to DCN1 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1301 b:17.9 occ:1.00 FBC A:DOJ1301 0.0 17.9 1.0 CBB A:DOJ1301 1.3 15.3 1.0 FBE A:DOJ1301 2.2 14.9 1.0 FBD A:DOJ1301 2.2 17.0 1.0 CAZ A:DOJ1301 2.3 13.5 1.0 HE2 A:PHE1089 2.7 20.0 1.0 HD2 A:PHE1089 2.9 18.0 1.0 HBA1 A:DOJ1301 3.0 15.7 1.0 CBA A:DOJ1301 3.0 13.1 1.0 CE2 A:PHE1089 3.2 16.7 1.0 CD2 A:PHE1089 3.3 15.0 1.0 CAY A:DOJ1301 3.3 13.6 1.0 HE2 A:PHE1117 3.4 15.9 1.0 HAY1 A:DOJ1301 3.5 16.4 1.0 CE2 A:PHE1117 3.6 13.2 1.0 HG22 A:ILE1105 3.7 16.1 1.0 HD2 A:PHE1117 3.7 15.1 1.0 CD2 A:PHE1117 3.8 12.5 1.0 HG21 A:ILE1105 3.9 16.1 1.0 HG23 A:ILE1086 3.9 16.1 1.0 HG13 A:VAL1102 4.2 18.8 1.0 CG2 A:ILE1105 4.3 13.4 1.0 CZ A:PHE1117 4.3 12.9 1.0 CAV A:DOJ1301 4.3 12.7 1.0 HG12 A:ILE1086 4.4 15.1 1.0 CZ A:PHE1089 4.4 16.8 1.0 CAX A:DOJ1301 4.5 12.8 1.0 HB A:ILE1105 4.5 14.1 1.0 CG A:PHE1089 4.5 13.1 1.0 HZ A:PHE1117 4.6 15.5 1.0 HB2 A:ALA1106 4.6 14.0 1.0 CG A:PHE1117 4.6 11.8 1.0 HG A:CYS1090 4.7 19.9 1.0 HB3 A:PHE1089 4.7 15.4 1.0 HZ A:PHE1089 4.7 20.1 1.0 HA A:ALA1106 4.7 13.5 1.0 CG2 A:ILE1086 4.9 13.4 1.0 CAW A:DOJ1301 4.9 12.3 1.0 HB2 A:PHE1117 4.9 14.1 1.0 HA A:ILE1086 5.0 15.0 1.0 CB A:ILE1105 5.0 11.8 1.0

Fluorine binding site 2 out of 3 in the Structure of (3S,4S)-1-Benzyl-4-(3-(3-(Trifluoromethyl)Phenyl)Ureido) Piperidin-3-Yl Acetate Bound to DCN1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of (3S,4S)-1-Benzyl-4-(3-(3-(Trifluoromethyl)Phenyl)Ureido) Piperidin-3-Yl Acetate Bound to DCN1 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1301 b:17.0 occ:1.00 FBD A:DOJ1301 0.0 17.0 1.0 CBB A:DOJ1301 1.4 15.3 1.0 FBE A:DOJ1301 2.2 14.9 1.0 FBC A:DOJ1301 2.2 17.9 1.0 CAZ A:DOJ1301 2.4 13.5 1.0 HAY1 A:DOJ1301 2.4 16.4 1.0 HG22 A:ILE1105 2.7 16.1 1.0 CAY A:DOJ1301 2.7 13.6 1.0 HA A:ALA1106 2.9 13.5 1.0 HB2 A:PHE1109 3.5 15.0 1.0 CG2 A:ILE1105 3.5 13.4 1.0 CZ A:PHE1117 3.6 12.9 1.0 HE2 A:PHE1089 3.6 20.0 1.0 CE2 A:PHE1117 3.6 13.2 1.0 HG21 A:ILE1105 3.6 16.1 1.0 CBA A:DOJ1301 3.7 13.1 1.0 CA A:ALA1106 3.7 11.3 1.0 HZ A:PHE1117 3.7 15.5 1.0 HB2 A:ALA1106 3.7 14.0 1.0 HE2 A:PHE1117 3.8 15.9 1.0 N A:ALA1106 3.8 11.2 1.0 HD1 A:PHE1109 3.9 16.9 1.0 HBA1 A:DOJ1301 4.0 15.7 1.0 C A:ILE1105 4.0 11.4 1.0 CE1 A:PHE1117 4.0 12.4 1.0 CD1 A:PHE1109 4.1 14.1 1.0 H A:ALA1106 4.1 13.5 1.0 O A:ILE1105 4.1 11.6 1.0 CD2 A:PHE1117 4.1 12.5 1.0 CAX A:DOJ1301 4.1 12.8 1.0 HG23 A:ILE1105 4.1 16.1 1.0 HB A:ILE1105 4.2 14.1 1.0 CG A:PHE1109 4.2 12.1 1.0 CB A:ALA1106 4.2 11.7 1.0 CB A:PHE1109 4.2 12.5 1.0 CE2 A:PHE1089 4.3 16.7 1.0 HE1 A:PHE1117 4.4 14.9 1.0 CB A:ILE1105 4.4 11.8 1.0 HB3 A:PHE1109 4.4 15.0 1.0 CD1 A:PHE1117 4.5 11.7 1.0 HB2 A:ALA1111 4.5 16.1 1.0 HD2 A:PHE1117 4.5 15.1 1.0 CG A:PHE1117 4.5 11.8 1.0 HB1 A:ALA1106 4.5 14.0 1.0 HAX1 A:DOJ1301 4.7 15.4 1.0 CE1 A:PHE1109 4.7 15.5 1.0 HD2 A:PHE1089 4.7 18.0 1.0 CAV A:DOJ1301 4.8 12.7 1.0 CA A:ILE1105 4.9 11.6 1.0 CD2 A:PHE1109 4.9 12.4 1.0 CD2 A:PHE1089 4.9 15.0 1.0 C A:ALA1106 4.9 11.0 1.0 CAW A:DOJ1301 5.0 12.3 1.0 HZ A:PHE1089 5.0 20.1 1.0

Fluorine binding site 3 out of 3 in the Structure of (3S,4S)-1-Benzyl-4-(3-(3-(Trifluoromethyl)Phenyl)Ureido) Piperidin-3-Yl Acetate Bound to DCN1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of (3S,4S)-1-Benzyl-4-(3-(3-(Trifluoromethyl)Phenyl)Ureido) Piperidin-3-Yl Acetate Bound to DCN1 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1301 b:14.9 occ:1.00 FBE A:DOJ1301 0.0 14.9 1.0 CBB A:DOJ1301 1.3 15.3 1.0 FBD A:DOJ1301 2.2 17.0 1.0 FBC A:DOJ1301 2.2 17.9 1.0 CAZ A:DOJ1301 2.4 13.5 1.0 HBA1 A:DOJ1301 2.7 15.7 1.0 HB2 A:ALA1106 2.8 14.0 1.0 CBA A:DOJ1301 2.9 13.1 1.0 HG22 A:ILE1105 3.0 16.1 1.0 H A:ALA1106 3.0 13.5 1.0 HB A:ILE1105 3.1 14.1 1.0 O A:VAL1102 3.1 12.1 1.0 N A:ALA1106 3.2 11.2 1.0 HA A:ALA1106 3.3 13.5 1.0 HG13 A:VAL1102 3.3 18.8 1.0 CAY A:DOJ1301 3.5 13.6 1.0 CA A:ALA1106 3.6 11.3 1.0 CG2 A:ILE1105 3.6 13.4 1.0 CB A:ALA1106 3.6 11.7 1.0 HG21 A:ILE1105 3.6 16.1 1.0 HAY1 A:DOJ1301 3.7 16.4 1.0 CB A:ILE1105 3.7 11.8 1.0 C A:ILE1105 3.8 11.4 1.0 HG12 A:VAL1102 3.9 18.8 1.0 O A:HOH1558 4.0 15.2 1.0 HE2 A:PHE1089 4.0 20.0 1.0 CG1 A:VAL1102 4.1 15.6 1.0 HB3 A:ALA1106 4.2 14.0 1.0 C A:VAL1102 4.2 11.9 1.0 CAV A:DOJ1301 4.2 12.7 1.0 HB1 A:ALA1106 4.2 14.0 1.0 HA A:VAL1102 4.3 15.3 1.0 CA A:ILE1105 4.4 11.6 1.0 OAT A:DOJ1301 4.4 14.8 1.0 HG23 A:ILE1105 4.5 16.1 1.0 O A:ILE1105 4.5 11.6 1.0 HD2 A:PHE1089 4.6 18.0 1.0 CAX A:DOJ1301 4.6 12.8 1.0 HG11 A:VAL1102 4.7 18.8 1.0 CA A:VAL1102 4.7 12.8 1.0 HD12 A:ILE1105 4.8 19.0 1.0 CE2 A:PHE1089 4.8 16.7 1.0 H A:ILE1105 4.9 13.6 1.0 HD13 A:ILE1105 4.9 19.0 1.0 CAW A:DOJ1301 4.9 12.3 1.0 N A:ILE1105 5.0 11.3 1.0

J.T.Hammill, D.C.Scott, J.Min, M.C.Connelly, G.Holbrook, F.Zhu, A.Matheny, L.Yang, B.Singh, B.A.Schulman, R.K.Guy. Piperidinyl Ureas Chemically Control Defective in Cullin Neddylation 1 (DCN1)-Mediated Cullin Neddylation. J. Med. Chem. V. 61 2680 2018.
ISSN: ISSN 1520-4804
PubMed: 29547696
DOI: 10.1021/ACS.JMEDCHEM.7B01277