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Bromine in PDB 5tcc: Complement Factor D Inhibited with JH4

Enzymatic activity of Complement Factor D Inhibited with JH4

All present enzymatic activity of Complement Factor D Inhibited with JH4:
3.4.21.46;

Protein crystallography data

The structure of Complement Factor D Inhibited with JH4, PDB code: 5tcc was solved by J.A.Stuckey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.86 / 3.37
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 98.886, 143.745, 346.166, 90.00, 90.00, 90.00
R / Rfree (%) 24.1 / 26

Bromine Binding Sites:

The binding sites of Bromine atom in the Complement Factor D Inhibited with JH4 (pdb code 5tcc). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 9 binding sites of Bromine where determined in the Complement Factor D Inhibited with JH4, PDB code: 5tcc:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Bromine binding site 1 out of 9 in 5tcc

Go back to Bromine Binding Sites List in 5tcc
Bromine binding site 1 out of 9 in the Complement Factor D Inhibited with JH4


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Complement Factor D Inhibited with JH4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br500

b:80.2
occ:1.00
 BR A:J56500 0.0 80.2 1.0
C A:J56500 1.9 73.0 1.0
N A:J56500 2.7 69.9 1.0
C17 A:J56500 2.8 70.3 1.0
O A:TRP143 3.5 39.8 1.0
CD2 A:HIS39 3.8 38.1 1.0
NH1 A:ARG152 3.9 45.0 1.0
CA A:GLY144 3.9 37.1 1.0
N A:ILE145 3.9 35.5 1.0
CA A:GLY196 4.0 28.2 1.0
CG A:ARG152 4.0 31.4 1.0
C1 A:J56500 4.0 68.7 1.0
CZ A:ARG152 4.0 51.2 1.0
O A:LYS195 4.1 31.5 1.0
C16 A:J56500 4.1 68.8 1.0
C A:GLY144 4.2 41.5 1.0
CG2 A:ILE145 4.3 37.5 1.0
C A:TRP143 4.4 41.1 1.0
NE2 A:HIS39 4.4 37.9 1.0
NH2 A:ARG152 4.4 20.6 1.0
NE A:ARG152 4.4 42.0 1.0
N A:GLY144 4.5 37.0 1.0
C15 A:J56500 4.6 68.8 1.0
N A:GLY196 4.7 28.7 1.0
C A:LYS195 4.7 32.4 1.0
CB A:ARG152 4.7 28.7 1.0
O A:HIS39 4.7 35.2 1.0
CD A:ARG152 4.7 36.3 1.0
C A:GLY196 4.8 31.6 1.0
CA A:ILE145 4.9 34.4 1.0
CG A:HIS39 4.9 36.6 1.0
O A:GLY196 5.0 31.0 1.0

Bromine binding site 2 out of 9 in 5tcc

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Bromine binding site 2 out of 9 in the Complement Factor D Inhibited with JH4


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Complement Factor D Inhibited with JH4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br500

b:77.9
occ:1.00
 BR B:J56500 0.0 77.9 1.0
C B:J56500 1.9 73.1 1.0
N B:J56500 2.7 71.8 1.0
C17 B:J56500 2.8 71.3 1.0
O B:TRP143 3.5 44.9 1.0
CD2 B:HIS39 3.8 39.2 1.0
CA B:GLY144 3.8 40.8 1.0
N B:ILE145 3.9 38.4 1.0
CA B:GLY196 3.9 27.6 1.0
C1 B:J56500 4.0 72.1 1.0
O B:LYS195 4.0 31.1 1.0
C16 B:J56500 4.1 72.7 1.0
C B:GLY144 4.2 43.9 1.0
CG2 B:ILE145 4.3 41.2 1.0
C B:TRP143 4.3 45.6 1.0
NE2 B:HIS39 4.4 38.8 1.0
N B:GLY144 4.5 41.6 1.0
C15 B:J56500 4.6 73.1 1.0
C B:LYS195 4.6 31.2 1.0
CB B:ARG152 4.6 24.8 1.0
N B:GLY196 4.6 27.5 1.0
O B:HIS39 4.8 42.1 1.0
CA B:ILE145 4.8 37.5 1.0
C B:GLY196 4.9 34.5 1.0
CG B:HIS39 5.0 37.9 1.0

Bromine binding site 3 out of 9 in 5tcc

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Bromine binding site 3 out of 9 in the Complement Factor D Inhibited with JH4


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Complement Factor D Inhibited with JH4 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Br301

b:95.9
occ:1.00
 BR C:J56301 0.0 95.9 1.0
C C:J56301 1.9 85.3 1.0
N C:J56301 2.7 79.7 1.0
C17 C:J56301 2.8 82.0 1.0
O C:TRP143 3.6 39.3 1.0
CA C:GLY144 3.8 36.0 1.0
CA C:GLY196 3.8 21.4 1.0
CD2 C:HIS39 3.8 47.6 1.0
N C:ILE145 3.9 33.2 1.0
O C:LYS195 4.0 21.8 1.0
C1 C:J56301 4.0 76.0 1.0
C16 C:J56301 4.1 80.8 1.0
C C:GLY144 4.2 39.6 1.0
CG2 C:ILE145 4.3 36.4 1.0
NE2 C:HIS39 4.4 47.5 1.0
C C:TRP143 4.4 40.5 1.0
N C:GLY144 4.5 36.4 1.0
N C:GLY196 4.6 20.4 1.0
C C:LYS195 4.6 22.8 1.0
C15 C:J56301 4.6 78.7 1.0
CB C:ARG152 4.7 25.6 1.0
C C:GLY196 4.8 28.2 1.0
O C:HIS39 4.8 50.1 1.0
CA C:ILE145 4.8 32.7 1.0
O C:GLY196 5.0 27.6 1.0
N1 C:J56301 5.0 72.2 1.0

Bromine binding site 4 out of 9 in 5tcc

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Bromine binding site 4 out of 9 in the Complement Factor D Inhibited with JH4


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Complement Factor D Inhibited with JH4 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Br302

b:0.5
occ:1.00
 BR C:J56302 0.0 0.5 1.0
C C:J56302 1.9 97.1 1.0
N C:J56302 2.8 88.0 1.0
C17 C:J56302 2.8 90.5 1.0
CE1 C:HIS158 3.4 44.8 1.0
CD C:ARG20 3.7 78.5 1.0
O C:HIS158 3.8 37.8 1.0
NE2 C:HIS158 3.9 45.5 1.0
CA C:VAL159 3.9 33.3 1.0
ND1 C:HIS158 3.9 44.8 1.0
N C:LEU160 3.9 36.8 1.0
C1 C:J56302 4.0 80.7 1.0
CD1 C:LEU160 4.0 39.4 1.0
C16 C:J56302 4.1 86.9 1.0
CG C:ARG20 4.3 60.0 1.0
CB C:ARG20 4.3 41.4 1.0
C C:VAL159 4.3 40.1 1.0
N C:ARG20 4.3 42.6 1.0
C C:HIS158 4.4 39.2 1.0
N C:VAL159 4.4 34.5 1.0
NE C:ARG20 4.5 89.7 1.0
CG C:LEU160 4.5 39.6 1.0
C15 C:J56302 4.6 83.8 1.0
CD2 C:HIS158 4.6 45.6 1.0
CB C:LEU160 4.6 35.6 1.0
CG C:HIS158 4.6 42.7 1.0
CG2 C:VAL159 4.9 35.6 1.0
CA C:LEU160 4.9 35.9 1.0
CA C:GLY19 4.9 42.7 1.0
CB C:VAL159 4.9 35.7 1.0
CA C:ARG20 5.0 41.8 1.0

Bromine binding site 5 out of 9 in 5tcc

Go back to Bromine Binding Sites List in 5tcc
Bromine binding site 5 out of 9 in the Complement Factor D Inhibited with JH4


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of Complement Factor D Inhibited with JH4 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Br500

b:90.7
occ:1.00
 BR D:J56500 0.0 90.7 1.0
C D:J56500 1.9 84.2 1.0
N D:J56500 2.8 80.0 1.0
C17 D:J56500 2.8 82.8 1.0
O D:TRP143 3.5 45.0 1.0
NH1 D:ARG152 3.7 44.0 1.0
CD2 D:HIS39 3.9 48.4 1.0
CA D:GLY144 3.9 42.5 1.0
CG D:ARG152 4.0 40.9 1.0
CZ D:ARG152 4.0 61.8 1.0
C1 D:J56500 4.0 76.8 1.0
N D:ILE145 4.0 39.6 1.0
CA D:GLY196 4.1 40.8 1.0
C16 D:J56500 4.1 82.1 1.0
O D:LYS195 4.2 44.1 1.0
CG2 D:ILE145 4.3 40.2 1.0
C D:GLY144 4.3 44.5 1.0
C D:TRP143 4.4 47.1 1.0
NE D:ARG152 4.4 47.4 1.0
NH2 D:ARG152 4.4 48.3 1.0
NE2 D:HIS39 4.6 48.2 1.0
N D:GLY144 4.6 43.2 1.0
C15 D:J56500 4.6 79.6 1.0
CB D:ARG152 4.6 40.9 1.0
CD D:ARG152 4.7 38.2 1.0
O D:HIS39 4.7 47.0 1.0
C D:LYS195 4.8 44.1 1.0
N D:GLY196 4.8 40.8 1.0
CA D:ILE145 4.9 38.8 1.0
CG D:HIS39 4.9 46.9 1.0
C D:GLY196 5.0 44.8 1.0

Bromine binding site 6 out of 9 in 5tcc

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Bromine binding site 6 out of 9 in the Complement Factor D Inhibited with JH4


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of Complement Factor D Inhibited with JH4 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Br301

b:94.1
occ:1.00
 BR E:J56301 0.0 94.1 1.0
C E:J56301 1.9 81.5 1.0
N E:J56301 2.8 75.9 1.0
C17 E:J56301 2.8 75.9 1.0
O E:TRP143 3.5 45.6 1.0
CD2 E:HIS39 3.7 41.7 1.0
CA E:GLY196 3.8 31.1 1.0
CA E:GLY144 3.8 37.5 1.0
N E:ILE145 4.0 36.0 1.0
NE2 E:HIS39 4.0 41.7 1.0
C1 E:J56301 4.0 71.9 1.0
O E:LYS195 4.1 36.4 1.0
C16 E:J56301 4.1 73.7 1.0
C E:GLY144 4.2 40.0 1.0
C E:TRP143 4.3 44.9 1.0
CG2 E:ILE145 4.4 38.7 1.0
N E:GLY144 4.5 38.4 1.0
N E:GLY196 4.6 31.8 1.0
C15 E:J56301 4.6 73.0 1.0
O E:HIS39 4.6 39.2 1.0
C E:LYS195 4.6 35.8 1.0
CB E:ARG152 4.7 30.8 1.0
C E:GLY196 4.7 35.5 1.0
O E:GLY196 4.9 35.1 1.0
CA E:ILE145 4.9 35.6 1.0
CG E:HIS39 5.0 40.3 1.0

Bromine binding site 7 out of 9 in 5tcc

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Bromine binding site 7 out of 9 in the Complement Factor D Inhibited with JH4


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 7 of Complement Factor D Inhibited with JH4 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Br302

b:0.0
occ:1.00
 BR E:J56302 0.0 0.0 1.0
C E:J56302 1.9 98.7 1.0
N E:J56302 2.7 96.2 1.0
C17 E:J56302 2.8 96.7 1.0
C1 E:J56302 4.0 93.0 1.0
CB D:ASP63 4.0 69.5 1.0
N D:ASP63 4.0 67.9 1.0
C16 E:J56302 4.1 94.5 1.0
O1 E:J56302 4.2 76.6 1.0
CG D:ASP63 4.2 81.0 1.0
CA D:ASP63 4.3 67.5 1.0
C D:ALA62 4.4 72.2 1.0
OD2 D:ASP63 4.4 84.2 1.0
N E:LEU160 4.4 49.6 1.0
CG2 E:VAL159 4.4 54.5 1.0
O E:GLY18 4.5 43.4 1.0
C15 E:J56302 4.6 93.4 1.0
CA E:VAL159 4.7 51.0 1.0
CA D:ALA62 4.8 69.8 1.0
CA E:GLY19 4.8 37.4 1.0
OD1 D:ASP63 4.8 82.2 1.0
N E:ARG20 4.8 34.3 1.0
O D:ALA62 4.9 71.5 1.0
N1 E:J56302 4.9 87.4 1.0
C2 E:J56302 5.0 79.1 1.0

Bromine binding site 8 out of 9 in 5tcc

Go back to Bromine Binding Sites List in 5tcc
Bromine binding site 8 out of 9 in the Complement Factor D Inhibited with JH4


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 8 of Complement Factor D Inhibited with JH4 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Br500

b:86.8
occ:1.00
 BR F:J56500 0.0 86.8 1.0
C F:J56500 1.9 76.8 1.0
N F:J56500 2.8 70.8 1.0
C17 F:J56500 2.8 73.3 1.0
O F:TRP143 3.5 51.2 1.0
NH1 F:ARG152 3.8 51.8 1.0
CD2 F:HIS39 3.9 41.0 1.0
CA F:GLY144 3.9 47.6 1.0
N F:ILE145 3.9 50.7 1.0
CA F:GLY196 3.9 34.4 1.0
CZ F:ARG152 4.0 65.0 1.0
CG F:ARG152 4.0 39.6 1.0
C1 F:J56500 4.0 66.2 1.0
C16 F:J56500 4.1 70.0 1.0
C F:GLY144 4.2 53.0 1.0
CG2 F:ILE145 4.2 54.5 1.0
O F:LYS195 4.3 38.9 1.0
NH2 F:ARG152 4.3 45.8 1.0
C F:TRP143 4.4 50.9 1.0
NE F:ARG152 4.4 49.4 1.0
NE2 F:HIS39 4.4 41.1 1.0
N F:GLY144 4.6 47.4 1.0
C15 F:J56500 4.6 67.1 1.0
N F:GLY196 4.7 35.1 1.0
CB F:ARG152 4.7 37.7 1.0
CD F:ARG152 4.7 35.2 1.0
O F:HIS39 4.7 40.0 1.0
C F:LYS195 4.8 39.3 1.0
CA F:ILE145 4.8 50.9 1.0
C F:GLY196 4.9 37.5 1.0

Bromine binding site 9 out of 9 in 5tcc

Go back to Bromine Binding Sites List in 5tcc
Bromine binding site 9 out of 9 in the Complement Factor D Inhibited with JH4


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 9 of Complement Factor D Inhibited with JH4 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Br500

b:76.6
occ:1.00
 BR G:J56500 0.0 76.6 1.0
C G:J56500 1.9 73.4 1.0
N G:J56500 2.8 72.7 1.0
C17 G:J56500 2.8 72.0 1.0
O G:TRP143 3.6 50.4 1.0
CD2 G:HIS39 3.9 48.5 1.0
CA G:GLY144 3.9 46.9 1.0
N G:ILE145 3.9 46.0 1.0
CZ G:ARG152 3.9 74.0 1.0
CA G:GLY196 4.0 41.8 1.0
CG G:ARG152 4.0 38.6 1.0
C1 G:J56500 4.0 72.8 1.0
NH2 G:ARG152 4.0 51.3 1.0
O G:LYS195 4.0 45.6 1.0
NE G:ARG152 4.1 51.5 1.0
C16 G:J56500 4.1 71.4 1.0
C G:GLY144 4.2 50.3 1.0
CG2 G:ILE145 4.3 49.1 1.0
NH1 G:ARG152 4.4 71.5 1.0
C G:TRP143 4.4 51.0 1.0
NE2 G:HIS39 4.4 48.4 1.0
N G:GLY144 4.6 47.2 1.0
C15 G:J56500 4.6 72.2 1.0
C G:LYS195 4.6 45.9 1.0
N G:GLY196 4.6 42.4 1.0
CD G:ARG152 4.7 39.6 1.0
O G:HIS39 4.8 46.7 1.0
CB G:ARG152 4.8 35.3 1.0
CA G:ILE145 4.8 45.4 1.0
C G:GLY196 4.9 45.5 1.0

Reference:

C.Y.Yang, J.G.Phillips, J.A.Stuckey, L.Bai, H.Sun, J.Delproposto, W.C.Brown, K.Chinnaswamy. Buried Hydrogen Bond Interactions Contribute to the High Potency of Complement Factor D Inhibitors. Acs Med Chem Lett V. 7 1092 2016.
ISSN: ISSN 1948-5875
PubMed: 27994744
DOI: 10.1021/ACSMEDCHEMLETT.6B00299
Page generated: Thu Jul 11 01:06:04 2024

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