Bromine in PDB 8dea: Scaffold Hopping Via Ring Opening Enables Identification of Acyclic Compounds As New Complement Factor D Inhibitors

Enzymatic activity of Scaffold Hopping Via Ring Opening Enables Identification of Acyclic Compounds As New Complement Factor D Inhibitors

All present enzymatic activity of Scaffold Hopping Via Ring Opening Enables Identification of Acyclic Compounds As New Complement Factor D Inhibitors:
3.4.21.46;

Protein crystallography data

The structure of Scaffold Hopping Via Ring Opening Enables Identification of Acyclic Compounds As New Complement Factor D Inhibitors, PDB code: 8dea was solved by K.Raman, Y.S.Babu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.46 / 2.21
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 44.898, 73.032, 240.864, 90, 90, 90
R / Rfree (%) 22.5 / 30

Bromine Binding Sites:

The binding sites of Bromine atom in the Scaffold Hopping Via Ring Opening Enables Identification of Acyclic Compounds As New Complement Factor D Inhibitors (pdb code 8dea). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 4 binding sites of Bromine where determined in the Scaffold Hopping Via Ring Opening Enables Identification of Acyclic Compounds As New Complement Factor D Inhibitors, PDB code: 8dea:
Jump to Bromine binding site number: 1; 2; 3; 4;

Bromine binding site 1 out of 4 in 8dea

Go back to Bromine Binding Sites List in 8dea
Bromine binding site 1 out of 4 in the Scaffold Hopping Via Ring Opening Enables Identification of Acyclic Compounds As New Complement Factor D Inhibitors


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Scaffold Hopping Via Ring Opening Enables Identification of Acyclic Compounds As New Complement Factor D Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br301

b:28.1
occ:1.00
 BR20 A:R7X301 0.0 28.1 1.0
C19 A:R7X301 2.0 29.5 1.0
N21 A:R7X301 2.9 31.5 1.0
C18 A:R7X301 3.0 28.3 1.0
O A:TRP128 3.4 20.1 1.0
O A:HOH403 3.8 24.6 1.0
CA A:GLY129 3.8 22.5 1.0
CD2 A:HIS24 3.9 30.3 1.0
CA A:GLY181 3.9 24.5 1.0
CG A:ARG137 4.0 34.1 1.0
C A:GLY129 4.1 22.8 1.0
CZ A:ARG137 4.1 42.4 1.0
N A:ILE130 4.2 25.2 1.0
O A:LYS180 4.2 25.6 1.0
C15 A:R7X301 4.2 30.5 1.0
C17 A:R7X301 4.2 29.4 1.0
C A:TRP128 4.3 20.4 1.0
NH1 A:ARG137 4.3 44.7 1.0
CG2 A:ILE130 4.3 26.1 1.0
NH2 A:ARG137 4.4 41.8 1.0
NE A:ARG137 4.4 40.3 1.0
N A:GLY129 4.5 20.4 1.0
NE2 A:HIS24 4.5 29.1 1.0
CD A:ARG137 4.6 36.6 1.0
CB A:ARG137 4.6 32.9 1.0
O A:HIS24 4.6 27.1 1.0
N A:GLY181 4.7 24.0 1.0
C16 A:R7X301 4.7 30.7 1.0
O A:GLY129 4.8 23.0 1.0
C A:GLY181 4.8 21.5 1.0
C A:LYS180 4.8 26.0 1.0
O A:GLY181 4.9 20.4 1.0
CA A:ILE130 4.9 26.1 1.0
CA A:ARG137 5.0 34.2 1.0

Bromine binding site 2 out of 4 in 8dea

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Bromine binding site 2 out of 4 in the Scaffold Hopping Via Ring Opening Enables Identification of Acyclic Compounds As New Complement Factor D Inhibitors


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Scaffold Hopping Via Ring Opening Enables Identification of Acyclic Compounds As New Complement Factor D Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br301

b:34.3
occ:1.00
 BR20 B:R7X301 0.0 34.3 1.0
C19 B:R7X301 1.9 28.8 1.0
N21 B:R7X301 2.8 27.6 1.0
C18 B:R7X301 2.9 28.9 1.0
O B:TRP128 3.3 24.6 1.0
CA B:GLY129 3.8 26.1 1.0
CG B:ARG137 3.9 37.1 1.0
N B:ILE130 3.9 24.4 1.0
CD2 B:HIS24 4.0 27.8 1.0
CA B:GLY181 4.0 27.3 1.0
C B:GLY129 4.0 24.4 1.0
O B:LYS180 4.1 28.9 1.0
C15 B:R7X301 4.1 29.5 1.0
O B:HOH407 4.1 23.3 1.0
C17 B:R7X301 4.1 28.0 1.0
CG2 B:ILE130 4.2 26.3 1.0
C B:TRP128 4.2 25.7 1.0
CZ B:ARG137 4.3 36.8 1.0
NE B:ARG137 4.3 43.4 1.0
NH1 B:ARG137 4.3 32.9 1.0
CD B:ARG137 4.4 39.0 1.0
N B:GLY129 4.5 24.2 1.0
CB B:ARG137 4.6 36.2 1.0
NE2 B:HIS24 4.6 24.1 1.0
C16 B:R7X301 4.6 28.1 1.0
C B:LYS180 4.7 30.0 1.0
N B:GLY181 4.7 26.9 1.0
CA B:ILE130 4.8 24.4 1.0
O B:HIS24 4.8 30.2 1.0
O B:GLY129 4.8 28.0 1.0
NH2 B:ARG137 4.8 38.4 1.0
C B:GLY181 4.9 26.7 1.0
CA B:ARG137 4.9 37.1 1.0

Bromine binding site 3 out of 4 in 8dea

Go back to Bromine Binding Sites List in 8dea
Bromine binding site 3 out of 4 in the Scaffold Hopping Via Ring Opening Enables Identification of Acyclic Compounds As New Complement Factor D Inhibitors


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Scaffold Hopping Via Ring Opening Enables Identification of Acyclic Compounds As New Complement Factor D Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Br301

b:31.5
occ:1.00
 BR20 C:R7X301 0.0 31.5 1.0
C19 C:R7X301 1.9 27.6 1.0
N21 C:R7X301 2.9 29.0 1.0
C18 C:R7X301 2.9 27.6 1.0
O C:TRP128 3.3 26.7 1.0
ND1 C:HIS24 3.7 26.0 1.0
O C:LYS180 4.0 27.2 1.0
CA C:GLY129 4.0 26.2 1.0
CA C:GLY181 4.1 28.0 1.0
N C:ILE130 4.1 24.9 1.0
CE1 C:HIS24 4.2 24.3 1.0
CG C:ARG137 4.2 37.1 1.0
C15 C:R7X301 4.2 29.1 1.0
C C:GLY129 4.2 23.8 1.0
C17 C:R7X301 4.2 26.5 1.0
C C:TRP128 4.3 25.9 1.0
CG2 C:ILE130 4.3 26.1 1.0
O C:HOH405 4.3 24.0 1.0
CB C:ARG137 4.5 34.1 1.0
NE C:ARG137 4.5 42.1 1.0
O C:HIS24 4.6 29.6 1.0
N C:GLY129 4.6 24.4 1.0
C C:LYS180 4.7 28.9 1.0
C16 C:R7X301 4.7 27.0 1.0
N C:GLY181 4.8 28.5 1.0
CZ C:ARG137 4.8 41.0 1.0
CG C:HIS24 4.9 24.8 1.0
CA C:ILE130 4.9 27.3 1.0
CA C:ARG137 4.9 32.2 1.0
NH2 C:ARG137 4.9 39.6 1.0
O C:GLY129 5.0 24.4 1.0
C C:GLY181 5.0 28.9 1.0
CD C:ARG137 5.0 41.3 1.0

Bromine binding site 4 out of 4 in 8dea

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Bromine binding site 4 out of 4 in the Scaffold Hopping Via Ring Opening Enables Identification of Acyclic Compounds As New Complement Factor D Inhibitors


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Scaffold Hopping Via Ring Opening Enables Identification of Acyclic Compounds As New Complement Factor D Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Br301

b:39.4
occ:1.00
 BR20 D:R7X301 0.0 39.4 1.0
C19 D:R7X301 2.0 43.2 1.0
N21 D:R7X301 2.9 48.6 1.0
C18 D:R7X301 3.0 42.6 1.0
O D:TRP128 3.6 27.1 1.0
CG D:ARG137 3.7 47.2 1.0
ND1 D:HIS24 3.9 32.6 1.0
NE D:ARG137 3.9 57.2 1.0
CA D:GLY129 3.9 30.4 1.0
CD1 D:ILE130 4.0 40.0 1.0
O D:LYS180 4.0 30.3 1.0
CZ D:ARG137 4.1 54.8 1.0
N D:ILE130 4.1 32.7 1.0
CD D:ARG137 4.2 49.6 1.0
CB D:ARG137 4.2 43.4 1.0
CA D:GLY181 4.2 26.7 1.0
C D:GLY129 4.2 32.1 1.0
C15 D:R7X301 4.3 46.2 1.0
NH2 D:ARG137 4.3 54.4 1.0
CE1 D:HIS24 4.3 30.8 1.0
C17 D:R7X301 4.4 43.4 1.0
O D:HIS24 4.4 30.5 1.0
C D:TRP128 4.4 25.7 1.0
CG1 D:ILE130 4.6 38.4 1.0
N D:GLY129 4.6 30.1 1.0
NH1 D:ARG137 4.7 50.2 1.0
C D:LYS180 4.8 30.5 1.0
CA D:ARG137 4.8 42.9 1.0
C16 D:R7X301 4.9 42.7 1.0
N D:GLY181 4.9 28.4 1.0

Reference:

W.Zhang, M.Wu, S.Vadlakonda, L.Juarez, X.Cheng, S.Muppa, V.Chintareddy, L.Vogeti, D.Kellogg-Yelder, J.Williams, K.Polach, X.Chen, K.Raman, Y.S.Babu, P.Kotian. Scaffold Hopping Via Ring Opening Enables Identification of Acyclic Compounds As New Complement Factor D Inhibitors. Bioorg.Med.Chem. V. 74 17034 2022.
ISSN: ESSN 1464-3391
PubMed: 36272185
DOI: 10.1016/J.BMC.2022.117034
Page generated: Thu Jul 11 05:02:38 2024

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