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Fluorine in PDB 3d3e: Crystal Structure of Human 11-Beta-Hydroxysteroid Dehydrogenase (HSD1) in Complex with Benzamide Inhibitor

Enzymatic activity of Crystal Structure of Human 11-Beta-Hydroxysteroid Dehydrogenase (HSD1) in Complex with Benzamide Inhibitor

All present enzymatic activity of Crystal Structure of Human 11-Beta-Hydroxysteroid Dehydrogenase (HSD1) in Complex with Benzamide Inhibitor:
1.1.1.146;

Protein crystallography data

The structure of Crystal Structure of Human 11-Beta-Hydroxysteroid Dehydrogenase (HSD1) in Complex with Benzamide Inhibitor, PDB code: 3d3e was solved by Z.Wang, A.Sudom, J.Liu, N.P.Walker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 66.37 / 2.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 56.700, 152.846, 73.708, 90.00, 92.11, 90.00
R / Rfree (%) 22.7 / 28.3

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Fluorine atom in the Crystal Structure of Human 11-Beta-Hydroxysteroid Dehydrogenase (HSD1) in Complex with Benzamide Inhibitor (pdb code 3d3e). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 12 binding sites of Fluorine where determined in the Crystal Structure of Human 11-Beta-Hydroxysteroid Dehydrogenase (HSD1) in Complex with Benzamide Inhibitor, PDB code: 3d3e:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 12 in 3d3e

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Fluorine binding site 1 out of 12 in the Crystal Structure of Human 11-Beta-Hydroxysteroid Dehydrogenase (HSD1) in Complex with Benzamide Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Human 11-Beta-Hydroxysteroid Dehydrogenase (HSD1) in Complex with Benzamide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F293

b:54.6
occ:1.00
 F25 A:D3E293 0.0 54.6 1.0
C21 A:D3E293 1.3 56.0 1.0
F24 A:D3E293 2.2 56.8 1.0
F23 A:D3E293 2.2 56.0 1.0
C2 A:D3E293 2.4 55.8 1.0
C3 A:D3E293 2.9 56.0 1.0
C8 A:D3E293 3.1 56.9 1.0
CD2 A:LEU126 3.1 49.4 1.0
C1 A:D3E293 3.2 55.3 1.0
O22 A:D3E293 3.5 54.5 1.0
O A:THR124 3.5 48.3 1.0
CG A:LEU126 3.6 50.0 1.0
C4 A:D3E293 3.9 56.1 1.0
C A:SER125 4.1 49.8 1.0
C7 A:D3E293 4.2 57.2 1.0
O A:SER125 4.2 50.2 1.0
C A:THR124 4.3 48.0 1.0
N A:LEU126 4.4 50.2 1.0
CD1 A:LEU126 4.4 49.5 1.0
CB A:ALA226 4.4 64.2 1.0
CA A:SER125 4.5 49.6 1.0
CB A:THR124 4.6 47.4 1.0
N A:SER125 4.8 48.8 1.0
CB A:LEU126 4.9 50.3 1.0
C5 A:D3E293 4.9 56.6 1.0
CA A:LEU126 4.9 50.4 1.0

Fluorine binding site 2 out of 12 in 3d3e

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Fluorine binding site 2 out of 12 in the Crystal Structure of Human 11-Beta-Hydroxysteroid Dehydrogenase (HSD1) in Complex with Benzamide Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Human 11-Beta-Hydroxysteroid Dehydrogenase (HSD1) in Complex with Benzamide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F293

b:56.0
occ:1.00
 F23 A:D3E293 0.0 56.0 1.0
C21 A:D3E293 1.3 56.0 1.0
F24 A:D3E293 2.1 56.8 1.0
F25 A:D3E293 2.2 54.6 1.0
C2 A:D3E293 2.3 55.8 1.0
O22 A:D3E293 2.3 54.5 1.0
C3 A:D3E293 3.0 56.0 1.0
CB A:ALA226 3.1 64.2 1.0
C4 A:D3E293 3.4 56.1 1.0
C1 A:D3E293 3.6 55.3 1.0
CA A:ALA223 3.9 57.9 1.0
C8 A:D3E293 4.0 56.9 1.0
O A:THR222 4.0 56.3 1.0
O A:ALA223 4.2 58.7 1.0
CG A:LEU126 4.3 50.0 1.0
CD2 A:LEU126 4.4 49.4 1.0
CD1 A:LEU126 4.5 49.5 1.0
CA A:ALA226 4.5 64.3 1.0
C A:ALA223 4.5 58.5 1.0
N A:ALA223 4.5 57.1 1.0
C A:THR222 4.5 56.6 1.0
O A:THR124 4.5 48.3 1.0
C5 A:D3E293 4.6 56.6 1.0
CB A:ALA223 4.7 57.9 1.0
N A:ALA226 4.8 63.6 1.0
CG2 A:THR222 4.8 55.6 1.0

Fluorine binding site 3 out of 12 in 3d3e

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Fluorine binding site 3 out of 12 in the Crystal Structure of Human 11-Beta-Hydroxysteroid Dehydrogenase (HSD1) in Complex with Benzamide Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Human 11-Beta-Hydroxysteroid Dehydrogenase (HSD1) in Complex with Benzamide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F293

b:56.8
occ:1.00
 F24 A:D3E293 0.0 56.8 1.0
C21 A:D3E293 1.3 56.0 1.0
F23 A:D3E293 2.1 56.0 1.0
F25 A:D3E293 2.2 54.6 1.0
C2 A:D3E293 2.4 55.8 1.0
O A:THR124 2.5 48.3 1.0
O22 A:D3E293 2.8 54.5 1.0
C1 A:D3E293 2.8 55.3 1.0
C A:THR124 3.7 48.0 1.0
C3 A:D3E293 3.7 56.0 1.0
CB A:ALA226 4.0 64.2 1.0
CG2 A:THR222 4.0 55.6 1.0
CA A:SER125 4.2 49.6 1.0
C8 A:D3E293 4.4 56.9 1.0
N A:SER125 4.4 48.8 1.0
O A:THR222 4.5 56.3 1.0
C A:SER125 4.7 49.8 1.0
C4 A:D3E293 4.7 56.1 1.0
CA A:THR124 4.7 47.5 1.0
CB A:THR124 4.7 47.4 1.0
N A:THR124 4.9 46.6 1.0
CG A:LEU126 4.9 50.0 1.0
C A:THR222 5.0 56.6 1.0
CD2 A:LEU126 5.0 49.4 1.0

Fluorine binding site 4 out of 12 in 3d3e

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Fluorine binding site 4 out of 12 in the Crystal Structure of Human 11-Beta-Hydroxysteroid Dehydrogenase (HSD1) in Complex with Benzamide Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Human 11-Beta-Hydroxysteroid Dehydrogenase (HSD1) in Complex with Benzamide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F293

b:61.3
occ:1.00
 F25 B:D3E293 0.0 61.3 1.0
C21 B:D3E293 1.3 61.5 1.0
F23 B:D3E293 2.1 61.5 1.0
F24 B:D3E293 2.2 61.4 1.0
C2 B:D3E293 2.4 61.5 1.0
C8 B:D3E293 2.8 61.2 1.0
C3 B:D3E293 2.8 61.1 1.0
C1 B:D3E293 3.1 61.3 1.0
CD2 B:LEU126 3.3 54.9 1.0
O22 B:D3E293 3.5 61.3 1.0
C B:SER125 3.9 54.4 1.0
CA B:SER125 3.9 53.8 1.0
C7 B:D3E293 4.0 61.3 1.0
C4 B:D3E293 4.0 61.0 1.0
N B:SER125 4.0 53.1 1.0
C B:THR124 4.1 52.2 1.0
O B:SER125 4.1 54.7 1.0
O B:THR124 4.2 52.4 1.0
N B:LEU126 4.3 54.9 1.0
CB B:THR124 4.3 51.6 1.0
CG B:LEU126 4.3 55.6 1.0
CB B:ALA226 4.6 62.7 1.0
CG2 B:THR124 4.9 51.5 1.0
C6 B:D3E293 4.9 61.4 1.0
CA B:THR124 4.9 51.5 1.0
C5 B:D3E293 4.9 61.2 1.0
CG1 B:VAL180 4.9 44.2 1.0

Fluorine binding site 5 out of 12 in 3d3e

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Fluorine binding site 5 out of 12 in the Crystal Structure of Human 11-Beta-Hydroxysteroid Dehydrogenase (HSD1) in Complex with Benzamide Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Human 11-Beta-Hydroxysteroid Dehydrogenase (HSD1) in Complex with Benzamide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F293

b:61.5
occ:1.00
 F23 B:D3E293 0.0 61.5 1.0
C21 B:D3E293 1.3 61.5 1.0
F25 B:D3E293 2.1 61.3 1.0
F24 B:D3E293 2.2 61.4 1.0
C2 B:D3E293 2.3 61.5 1.0
O22 B:D3E293 2.6 61.3 1.0
CB B:ALA226 2.8 62.7 1.0
C3 B:D3E293 2.9 61.1 1.0
C4 B:D3E293 3.5 61.0 1.0
CD2 B:LEU126 3.6 54.9 1.0
C8 B:D3E293 3.7 61.2 1.0
C1 B:D3E293 3.7 61.3 1.0
CG B:LEU126 4.1 55.6 1.0
CA B:ALA226 4.2 62.8 1.0
O B:THR222 4.6 51.8 1.0
C5 B:D3E293 4.6 61.2 1.0
CA B:ALA223 4.6 54.0 1.0
C7 B:D3E293 4.7 61.3 1.0
O B:ALA223 4.7 55.0 1.0
CD1 B:LEU126 4.7 55.7 1.0
C B:ALA226 4.7 63.7 1.0
CA B:SER125 4.8 53.8 1.0
N B:LEU126 4.9 54.9 1.0
C B:SER125 5.0 54.4 1.0
N B:ALA226 5.0 61.5 1.0
O B:THR124 5.0 52.4 1.0

Fluorine binding site 6 out of 12 in 3d3e

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Fluorine binding site 6 out of 12 in the Crystal Structure of Human 11-Beta-Hydroxysteroid Dehydrogenase (HSD1) in Complex with Benzamide Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Human 11-Beta-Hydroxysteroid Dehydrogenase (HSD1) in Complex with Benzamide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F293

b:61.4
occ:1.00
 F24 B:D3E293 0.0 61.4 1.0
C21 B:D3E293 1.3 61.5 1.0
F25 B:D3E293 2.2 61.3 1.0
F23 B:D3E293 2.2 61.5 1.0
C2 B:D3E293 2.4 61.5 1.0
O22 B:D3E293 2.8 61.3 1.0
C1 B:D3E293 2.8 61.3 1.0
O B:THR124 3.0 52.4 1.0
CB B:ALA226 3.5 62.7 1.0
C B:THR124 3.5 52.2 1.0
C3 B:D3E293 3.7 61.1 1.0
CA B:SER125 3.7 53.8 1.0
N B:SER125 3.9 53.1 1.0
CG2 B:THR222 4.1 51.1 1.0
C8 B:D3E293 4.3 61.2 1.0
C B:SER125 4.5 54.4 1.0
CA B:THR124 4.6 51.5 1.0
CB B:THR124 4.6 51.6 1.0
C4 B:D3E293 4.7 61.0 1.0
O B:THR222 4.7 51.8 1.0
N B:THR124 4.8 50.4 1.0
CD2 B:LEU126 4.9 54.9 1.0
N B:LEU126 4.9 54.9 1.0
CB B:SER125 4.9 54.0 1.0
CA B:ALA226 5.0 62.8 1.0

Fluorine binding site 7 out of 12 in 3d3e

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Fluorine binding site 7 out of 12 in the Crystal Structure of Human 11-Beta-Hydroxysteroid Dehydrogenase (HSD1) in Complex with Benzamide Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of Human 11-Beta-Hydroxysteroid Dehydrogenase (HSD1) in Complex with Benzamide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F293

b:74.3
occ:1.00
 F25 C:D3E293 0.0 74.3 1.0
C21 C:D3E293 1.3 74.4 1.0
F23 C:D3E293 2.2 74.5 1.0
F24 C:D3E293 2.2 74.7 1.0
C2 C:D3E293 2.4 73.8 1.0
C3 C:D3E293 2.9 73.2 1.0
C1 C:D3E293 3.1 73.5 1.0
C8 C:D3E293 3.1 73.1 1.0
O22 C:D3E293 3.5 73.9 1.0
C C:SER125 3.9 56.7 1.0
CA C:SER125 3.9 56.2 1.0
CD2 C:LEU126 4.0 57.0 1.0
C4 C:D3E293 4.0 73.3 1.0
N C:LEU126 4.0 57.3 1.0
N C:SER125 4.1 55.8 1.0
C C:THR124 4.2 55.3 1.0
O C:THR124 4.3 55.3 1.0
C7 C:D3E293 4.3 73.3 1.0
O C:SER125 4.3 56.6 1.0
CB C:THR124 4.4 54.8 1.0
CG C:LEU126 4.4 58.0 1.0
CB C:ALA226 4.5 73.6 1.0
CG2 C:VAL180 4.8 46.3 1.0
CA C:LEU126 4.8 58.0 1.0
OG1 C:THR124 4.9 55.8 1.0
C5 C:D3E293 5.0 73.3 1.0
CA C:THR124 5.0 54.8 1.0

Fluorine binding site 8 out of 12 in 3d3e

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Fluorine binding site 8 out of 12 in the Crystal Structure of Human 11-Beta-Hydroxysteroid Dehydrogenase (HSD1) in Complex with Benzamide Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of Human 11-Beta-Hydroxysteroid Dehydrogenase (HSD1) in Complex with Benzamide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F293

b:74.5
occ:1.00
 F23 C:D3E293 0.0 74.5 1.0
C21 C:D3E293 1.3 74.4 1.0
F25 C:D3E293 2.2 74.3 1.0
F24 C:D3E293 2.2 74.7 1.0
C2 C:D3E293 2.3 73.8 1.0
O22 C:D3E293 2.5 73.9 1.0
C3 C:D3E293 2.9 73.2 1.0
CB C:ALA226 3.1 73.6 1.0
C4 C:D3E293 3.3 73.3 1.0
C1 C:D3E293 3.7 73.5 1.0
C8 C:D3E293 3.8 73.1 1.0
O C:ALA223 4.2 67.5 1.0
CA C:ALA223 4.3 66.8 1.0
CA C:ALA226 4.3 73.7 1.0
C C:ALA226 4.4 74.3 1.0
C5 C:D3E293 4.4 73.3 1.0
O C:ALA226 4.5 74.4 1.0
CG1 C:VAL227 4.6 75.8 1.0
O C:THR222 4.6 65.0 1.0
CG C:LEU126 4.7 58.0 1.0
CD2 C:LEU126 4.7 57.0 1.0
C C:ALA223 4.7 67.5 1.0
C7 C:D3E293 4.8 73.3 1.0
CB C:ALA223 4.9 66.7 1.0
N C:VAL227 4.9 75.2 1.0

Fluorine binding site 9 out of 12 in 3d3e

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Fluorine binding site 9 out of 12 in the Crystal Structure of Human 11-Beta-Hydroxysteroid Dehydrogenase (HSD1) in Complex with Benzamide Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Crystal Structure of Human 11-Beta-Hydroxysteroid Dehydrogenase (HSD1) in Complex with Benzamide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F293

b:74.7
occ:1.00
 F24 C:D3E293 0.0 74.7 1.0
C21 C:D3E293 1.3 74.4 1.0
F25 C:D3E293 2.2 74.3 1.0
F23 C:D3E293 2.2 74.5 1.0
C2 C:D3E293 2.3 73.8 1.0
O22 C:D3E293 2.7 73.9 1.0
C1 C:D3E293 2.8 73.5 1.0
O C:THR124 3.0 55.3 1.0
CB C:ALA226 3.3 73.6 1.0
C C:THR124 3.6 55.3 1.0
C3 C:D3E293 3.7 73.2 1.0
CA C:SER125 3.8 56.2 1.0
N C:SER125 3.9 55.8 1.0
C8 C:D3E293 4.4 73.1 1.0
O C:THR222 4.5 65.0 1.0
C C:SER125 4.5 56.7 1.0
CB C:THR124 4.5 54.8 1.0
CG2 C:THR222 4.5 64.1 1.0
CA C:THR124 4.5 54.8 1.0
C4 C:D3E293 4.6 73.3 1.0
N C:LEU126 4.8 57.3 1.0
CA C:ALA226 4.8 73.7 1.0
N C:THR124 4.9 53.8 1.0
CB C:SER125 4.9 56.1 1.0
OG1 C:THR124 4.9 55.8 1.0

Fluorine binding site 10 out of 12 in 3d3e

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Fluorine binding site 10 out of 12 in the Crystal Structure of Human 11-Beta-Hydroxysteroid Dehydrogenase (HSD1) in Complex with Benzamide Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Crystal Structure of Human 11-Beta-Hydroxysteroid Dehydrogenase (HSD1) in Complex with Benzamide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F293

b:69.7
occ:1.00
 F25 D:D3E293 0.0 69.7 1.0
C21 D:D3E293 1.3 70.5 1.0
F23 D:D3E293 2.1 71.2 1.0
F24 D:D3E293 2.2 70.7 1.0
C2 D:D3E293 2.4 70.2 1.0
C3 D:D3E293 2.9 69.8 1.0
C8 D:D3E293 3.0 69.5 1.0
C1 D:D3E293 3.1 70.2 1.0
CD2 D:LEU126 3.5 59.6 1.0
O22 D:D3E293 3.5 70.2 1.0
CA D:SER125 3.9 60.2 1.0
C D:SER125 3.9 60.1 1.0
N D:LEU126 3.9 60.0 1.0
N D:SER125 4.0 60.3 1.0
C4 D:D3E293 4.0 69.6 1.0
O D:THR124 4.1 60.5 1.0
CG D:LEU126 4.1 59.9 1.0
C D:THR124 4.1 60.5 1.0
C7 D:D3E293 4.2 69.5 1.0
CB D:THR124 4.4 60.6 1.0
O D:SER125 4.4 60.1 1.0
CB D:ALA226 4.6 81.8 1.0
CA D:LEU126 4.7 60.0 1.0
CG1 D:VAL180 4.9 45.3 1.0
CA D:THR124 4.9 60.6 1.0
C5 D:D3E293 5.0 69.7 1.0

Reference:

L.D.Julian, Z.Wang, T.Bostick, S.Caille, R.Choi, M.Degraffenreid, Y.Di, X.He, R.W.Hungate, J.C.Jaen, J.Liu, M.Monshouwer, D.Mcminn, Y.Rew, A.Sudom, D.Sun, H.Tu, S.Ursu, N.Walker, X.Yan, Q.Ye, J.P.Powers. Discovery of Novel, Potent Benzamide Inhibitors of 11BETA-Hydroxysteroid Dehydrogenase Type 1 (11BETA-HSD1) Exhibiting Oral Activity in An Enzyme Inhibition Ex Vivo Model J.Med.Chem. V. 51 3953 2008.
ISSN: ISSN 0022-2623
PubMed: 18553955
DOI: 10.1021/JM800310G
Page generated: Wed Jul 31 17:51:31 2024

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