Atomistry » Fluorine » PDB 6b3c-6bgx » 6bg5
Atomistry »
  Fluorine »
    PDB 6b3c-6bgx »
      6bg5 »

Fluorine in PDB 6bg5: Structure of 1-(Benzo[D][1,3]Dioxol-5-Ylmethyl)-1-(1-Propylpiperidin- 4-Yl)-3-(3-(Trifluoromethyl)Phenyl)Urea Bound to DCN1

Enzymatic activity of Structure of 1-(Benzo[D][1,3]Dioxol-5-Ylmethyl)-1-(1-Propylpiperidin- 4-Yl)-3-(3-(Trifluoromethyl)Phenyl)Urea Bound to DCN1

All present enzymatic activity of Structure of 1-(Benzo[D][1,3]Dioxol-5-Ylmethyl)-1-(1-Propylpiperidin- 4-Yl)-3-(3-(Trifluoromethyl)Phenyl)Urea Bound to DCN1:
3.2.1.17;

Protein crystallography data

The structure of Structure of 1-(Benzo[D][1,3]Dioxol-5-Ylmethyl)-1-(1-Propylpiperidin- 4-Yl)-3-(3-(Trifluoromethyl)Phenyl)Urea Bound to DCN1, PDB code: 6bg5 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) 49.17 / 1.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 34.944, 96.763, 59.279, 90.00, 105.61, 90.00
R / Rfree (%) 14.6 / 17.2

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of 1-(Benzo[D][1,3]Dioxol-5-Ylmethyl)-1-(1-Propylpiperidin- 4-Yl)-3-(3-(Trifluoromethyl)Phenyl)Urea Bound to DCN1 (pdb code 6bg5). 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 1-(Benzo[D][1,3]Dioxol-5-Ylmethyl)-1-(1-Propylpiperidin- 4-Yl)-3-(3-(Trifluoromethyl)Phenyl)Urea Bound to DCN1, PDB code: 6bg5:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 6bg5

Go back to Fluorine Binding Sites List in 6bg5
Fluorine binding site 1 out of 3 in the Structure of 1-(Benzo[D][1,3]Dioxol-5-Ylmethyl)-1-(1-Propylpiperidin- 4-Yl)-3-(3-(Trifluoromethyl)Phenyl)Urea 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 1-(Benzo[D][1,3]Dioxol-5-Ylmethyl)-1-(1-Propylpiperidin- 4-Yl)-3-(3-(Trifluoromethyl)Phenyl)Urea Bound to DCN1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1301

b:16.2
occ:1.00
FBE A:DQD1301 0.0 16.2 1.0
CBD A:DQD1301 1.3 11.8 1.0
FBG A:DQD1301 2.1 12.2 1.0
FBF A:DQD1301 2.1 14.1 1.0
CBB A:DQD1301 2.4 10.2 1.0
HE2 A:PHE1089 2.8 16.7 1.0
HD2 A:PHE1089 2.8 14.3 1.0
CBC A:DQD1301 2.9 9.9 1.0
HG23 A:ILE1086 3.2 13.4 1.0
CE2 A:PHE1089 3.3 13.9 1.0
CD2 A:PHE1089 3.4 11.9 1.0
CBA A:DQD1301 3.4 10.5 1.0
HG13 A:VAL1102 3.6 13.4 1.0
HE2 A:PHE1117 4.0 12.5 1.0
HG22 A:ILE1105 4.0 13.3 1.0
HG21 A:ILE1105 4.1 13.3 1.0
HG A:CYS1090 4.1 13.7 1.0
CG2 A:ILE1086 4.1 11.1 1.0
HD2 A:PHE1117 4.1 12.2 1.0
CE2 A:PHE1117 4.2 10.4 1.0
CAX A:DQD1301 4.2 9.4 1.0
CD2 A:PHE1117 4.3 10.2 1.0
HG12 A:ILE1086 4.3 11.5 1.0
HG21 A:ILE1086 4.3 13.4 1.0
CG2 A:ILE1105 4.5 11.1 1.0
HB A:ILE1105 4.5 11.6 1.0
CG1 A:VAL1102 4.5 11.2 1.0
CZ A:PHE1089 4.6 13.8 1.0
HG22 A:ILE1086 4.6 13.4 1.0
CAZ A:DQD1301 4.6 9.8 1.0
HB2 A:ALA1106 4.6 11.1 1.0
CG A:PHE1089 4.7 10.0 1.0
HB3 A:PHE1089 4.7 11.9 1.0
HG12 A:VAL1102 4.7 13.4 1.0
SG A:CYS1090 4.8 11.4 1.0
HG11 A:VAL1102 4.8 13.4 1.0
HA A:ILE1086 4.8 11.2 1.0
CZ A:PHE1117 4.9 11.0 1.0
O A:VAL1102 4.9 10.4 1.0
HZ A:PHE1089 4.9 16.5 1.0
CAY A:DQD1301 4.9 9.6 1.0
HA A:ALA1106 5.0 11.4 1.0

Fluorine binding site 2 out of 3 in 6bg5

Go back to Fluorine Binding Sites List in 6bg5
Fluorine binding site 2 out of 3 in the Structure of 1-(Benzo[D][1,3]Dioxol-5-Ylmethyl)-1-(1-Propylpiperidin- 4-Yl)-3-(3-(Trifluoromethyl)Phenyl)Urea 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 1-(Benzo[D][1,3]Dioxol-5-Ylmethyl)-1-(1-Propylpiperidin- 4-Yl)-3-(3-(Trifluoromethyl)Phenyl)Urea Bound to DCN1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1301

b:14.1
occ:1.00
FBF A:DQD1301 0.0 14.1 1.0
CBD A:DQD1301 1.3 11.8 1.0
FBG A:DQD1301 2.1 12.2 1.0
FBE A:DQD1301 2.1 16.2 1.0
CBB A:DQD1301 2.4 10.2 1.0
HG22 A:ILE1105 2.7 13.3 1.0
CBA A:DQD1301 2.7 10.5 1.0
HE2 A:PHE1089 3.2 16.7 1.0
HA A:ALA1106 3.2 11.4 1.0
CG2 A:ILE1105 3.5 11.1 1.0
HG21 A:ILE1105 3.5 13.3 1.0
CE2 A:PHE1117 3.6 10.4 1.0
CBC A:DQD1301 3.7 9.9 1.0
HE2 A:PHE1117 3.7 12.5 1.0
CZ A:PHE1117 3.7 11.0 1.0
HB2 A:ALA1106 3.8 11.1 1.0
HZ A:PHE1117 3.9 13.2 1.0
CE2 A:PHE1089 3.9 13.9 1.0
CA A:ALA1106 3.9 9.5 1.0
N A:ALA1106 3.9 8.8 1.0
CD2 A:PHE1117 4.0 10.2 1.0
HB2 A:PHE1109 4.1 11.9 1.0
HB A:ILE1105 4.1 11.6 1.0
CAZ A:DQD1301 4.1 9.8 1.0
H A:ALA1106 4.1 10.6 1.0
HG23 A:ILE1105 4.2 13.3 1.0
CE1 A:PHE1117 4.2 10.3 1.0
C A:ILE1105 4.2 9.1 1.0
HD2 A:PHE1117 4.3 12.2 1.0
CB A:ALA1106 4.3 9.2 1.0
CB A:ILE1105 4.4 9.6 1.0
HD2 A:PHE1089 4.4 14.3 1.0
O A:ILE1105 4.4 9.2 1.0
HD1 A:PHE1109 4.4 14.8 1.0
CG A:PHE1117 4.5 9.3 1.0
CD2 A:PHE1089 4.6 11.9 1.0
CD1 A:PHE1117 4.6 9.8 1.0
CD1 A:PHE1109 4.6 12.4 1.0
HE1 A:PHE1117 4.6 12.4 1.0
HZ A:PHE1089 4.7 16.5 1.0
CZ A:PHE1089 4.7 13.8 1.0
HB1 A:ALA1106 4.7 11.1 1.0
HB2 A:ALA1111 4.7 12.8 1.0
CG A:PHE1109 4.8 9.9 1.0
CAX A:DQD1301 4.8 9.4 1.0
CB A:PHE1109 4.8 9.9 1.0
O A:VAL1102 4.8 10.4 1.0
HG13 A:VAL1102 4.9 13.4 1.0
CA A:ILE1105 5.0 9.2 1.0
CAY A:DQD1301 5.0 9.6 1.0
HB3 A:PHE1109 5.0 11.9 1.0

Fluorine binding site 3 out of 3 in 6bg5

Go back to Fluorine Binding Sites List in 6bg5
Fluorine binding site 3 out of 3 in the Structure of 1-(Benzo[D][1,3]Dioxol-5-Ylmethyl)-1-(1-Propylpiperidin- 4-Yl)-3-(3-(Trifluoromethyl)Phenyl)Urea 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 1-(Benzo[D][1,3]Dioxol-5-Ylmethyl)-1-(1-Propylpiperidin- 4-Yl)-3-(3-(Trifluoromethyl)Phenyl)Urea Bound to DCN1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1301

b:12.2
occ:1.00
FBG A:DQD1301 0.0 12.2 1.0
CBD A:DQD1301 1.3 11.8 1.0
FBE A:DQD1301 2.1 16.2 1.0
FBF A:DQD1301 2.1 14.1 1.0
CBB A:DQD1301 2.4 10.2 1.0
HB2 A:ALA1106 2.8 11.1 1.0
CBC A:DQD1301 2.9 9.9 1.0
O A:VAL1102 3.0 10.4 1.0
HG13 A:VAL1102 3.0 13.4 1.0
H A:ALA1106 3.1 10.6 1.0
HB A:ILE1105 3.2 11.6 1.0
HG22 A:ILE1105 3.2 13.3 1.0
N A:ALA1106 3.4 8.8 1.0
CBA A:DQD1301 3.5 10.5 1.0
HA A:ALA1106 3.5 11.4 1.0
HG12 A:VAL1102 3.6 13.4 1.0
CB A:ALA1106 3.6 9.2 1.0
CA A:ALA1106 3.7 9.5 1.0
CG1 A:VAL1102 3.7 11.2 1.0
HG21 A:ILE1105 3.8 13.3 1.0
CG2 A:ILE1105 3.8 11.1 1.0
CB A:ILE1105 3.9 9.6 1.0
HE2 A:PHE1089 3.9 16.7 1.0
C A:VAL1102 4.0 9.3 1.0
C A:ILE1105 4.0 9.1 1.0
O A:HOH1468 4.1 13.6 1.0
HA A:VAL1102 4.1 10.7 1.0
HB3 A:ALA1106 4.2 11.1 1.0
CAX A:DQD1301 4.3 9.4 1.0
HB1 A:ALA1106 4.3 11.1 1.0
HG11 A:VAL1102 4.4 13.4 1.0
CA A:VAL1102 4.5 8.9 1.0
CA A:ILE1105 4.5 9.2 1.0
OAV A:DQD1301 4.6 12.0 1.0
CAZ A:DQD1301 4.7 9.8 1.0
HG23 A:ILE1105 4.7 13.3 1.0
CB A:VAL1102 4.7 10.1 1.0
HD2 A:PHE1089 4.7 14.3 1.0
CE2 A:PHE1089 4.7 13.9 1.0
HG23 A:ILE1086 4.8 13.4 1.0
HD12 A:ILE1105 4.8 15.0 1.0
O A:ILE1105 4.8 9.2 1.0
HA A:LEU1103 4.8 11.2 1.0
H A:ILE1105 4.9 10.2 1.0
CAY A:DQD1301 5.0 9.6 1.0
HG22 A:VAL1102 5.0 13.1 1.0

Reference:

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
Page generated: Thu Aug 1 18:08:13 2024

Last articles

Cl in 3N54
Cl in 3N5J
Cl in 3N5L
Cl in 3N5H
Cl in 3N5C
Cl in 3N4E
Cl in 3N4A
Cl in 3N2L
Cl in 3N3Z
Cl in 3N2S
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy