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Fluorine in PDB 3cdb: Thermodynamic and Structure Guided Design of Statin Hmg-Coa Reductase Inhibitors

Enzymatic activity of Thermodynamic and Structure Guided Design of Statin Hmg-Coa Reductase Inhibitors

All present enzymatic activity of Thermodynamic and Structure Guided Design of Statin Hmg-Coa Reductase Inhibitors:
1.1.1.34;

Protein crystallography data

The structure of Thermodynamic and Structure Guided Design of Statin Hmg-Coa Reductase Inhibitors, PDB code: 3cdb was solved by A.Pavlovsky, R.W.Sarver, M.S.Harris, B.C.Finzel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 73.575, 173.484, 75.990, 90.00, 118.68, 90.00
R / Rfree (%) 20.2 / 23.9

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Thermodynamic and Structure Guided Design of Statin Hmg-Coa Reductase Inhibitors (pdb code 3cdb). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Thermodynamic and Structure Guided Design of Statin Hmg-Coa Reductase Inhibitors, PDB code: 3cdb:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 3cdb

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Fluorine binding site 1 out of 8 in the Thermodynamic and Structure Guided Design of Statin Hmg-Coa Reductase Inhibitors


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Thermodynamic and Structure Guided Design of Statin Hmg-Coa Reductase Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1

b:50.7
occ:1.00
 F2 A:9HI1 0.0 50.7 1.0
C28 A:9HI1 1.3 49.9 1.0
C22 A:9HI1 2.3 49.2 1.0
C19 A:9HI1 2.4 49.6 1.0
CA A:HIS861 2.7 51.0 1.0
N A:HIS861 2.7 49.9 1.0
O A:ALA856 3.0 33.7 1.0
CD2 A:HIS861 3.4 54.8 1.0
C A:HIS861 3.5 51.1 1.0
C25 A:9HI1 3.6 48.3 1.0
C16 A:9HI1 3.6 48.7 1.0
C A:ALA856 3.6 33.5 1.0
O A:HIS861 3.7 51.5 1.0
CB A:HIS861 3.9 51.3 1.0
C A:GLY860 3.9 48.6 1.0
CG A:HIS861 4.0 53.1 1.0
C31 A:9HI1 4.1 47.2 1.0
N A:LEU857 4.2 34.5 1.0
CA A:LEU857 4.2 35.1 1.0
O A:HOH907 4.3 31.2 1.0
CB A:ALA856 4.4 32.5 1.0
CA A:GLY860 4.5 47.3 1.0
CA A:ALA856 4.5 32.6 1.0
N A:GLY860 4.6 46.0 1.0
NE2 A:HIS861 4.6 55.5 1.0
O A:GLY860 4.8 48.9 1.0

Fluorine binding site 2 out of 8 in 3cdb

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Fluorine binding site 2 out of 8 in the Thermodynamic and Structure Guided Design of Statin Hmg-Coa Reductase Inhibitors


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Thermodynamic and Structure Guided Design of Statin Hmg-Coa Reductase Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1

b:40.4
occ:1.00
 F1 A:9HI1 0.0 40.4 1.0
C30 A:9HI1 1.3 41.4 1.0
C15 A:9HI1 2.4 41.8 1.0
C24 A:9HI1 2.4 42.3 1.0
NH1 B:ARG590 3.0 30.5 1.0
CD B:ARG590 3.1 32.3 1.0
CZ B:ARG590 3.2 32.1 1.0
NE B:ARG590 3.2 32.8 1.0
CG1 B:VAL683 3.2 28.8 1.0
C18 A:9HI1 3.6 42.2 1.0
C21 A:9HI1 3.6 42.5 1.0
NH2 B:ARG590 4.0 32.3 1.0
CB B:SER661 4.1 39.8 1.0
C27 A:9HI1 4.1 42.5 1.0
CG2 B:VAL683 4.1 29.4 1.0
CB B:VAL683 4.2 28.8 1.0
CG B:ARG590 4.3 31.0 1.0
CB B:SER684 4.3 26.9 1.0
C B:VAL683 4.3 27.9 1.0
O B:VAL683 4.3 27.6 1.0
N B:SER684 4.4 27.4 1.0
O B:HOH984 4.5 55.6 1.0
CA B:SER684 4.9 26.8 1.0
CA B:VAL683 4.9 28.6 1.0
OG B:SER661 5.0 40.2 1.0

Fluorine binding site 3 out of 8 in 3cdb

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Fluorine binding site 3 out of 8 in the Thermodynamic and Structure Guided Design of Statin Hmg-Coa Reductase Inhibitors


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Thermodynamic and Structure Guided Design of Statin Hmg-Coa Reductase Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2

b:45.3
occ:1.00
 F2 A:9HI2 0.0 45.3 1.0
C28 A:9HI2 1.3 45.8 1.0
C19 A:9HI2 2.4 46.2 1.0
C22 A:9HI2 2.4 45.6 1.0
O B:GLY860 2.7 49.3 1.0
C B:HIS861 3.6 51.7 1.0
C16 A:9HI2 3.6 46.0 1.0
C25 A:9HI2 3.6 45.3 1.0
O B:ALA856 3.7 31.4 1.0
CB B:HIS861 3.8 52.0 1.0
C B:GLY860 3.9 49.1 1.0
O B:HIS861 3.9 52.0 1.0
C31 A:9HI2 4.1 45.1 1.0
CA B:HIS861 4.2 51.6 1.0
N B:HIS861 4.5 50.5 1.0
C B:ALA856 4.5 31.4 1.0
ND1 B:HIS861 4.8 55.6 1.0
CG B:HIS861 4.8 53.7 1.0

Fluorine binding site 4 out of 8 in 3cdb

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Fluorine binding site 4 out of 8 in the Thermodynamic and Structure Guided Design of Statin Hmg-Coa Reductase Inhibitors


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Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Thermodynamic and Structure Guided Design of Statin Hmg-Coa Reductase Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2

b:45.6
occ:1.00
 F1 A:9HI2 0.0 45.6 1.0
C30 A:9HI2 1.3 44.8 1.0
C24 A:9HI2 2.3 44.9 1.0
C15 A:9HI2 2.4 44.2 1.0
NE A:ARG590 2.9 26.0 1.0
CZ A:ARG590 3.1 26.0 1.0
CD A:ARG590 3.4 26.4 1.0
NH2 A:ARG590 3.5 26.3 1.0
CG1 A:VAL683 3.5 27.9 1.0
C21 A:9HI2 3.6 44.4 1.0
C18 A:9HI2 3.6 44.3 1.0
NH1 A:ARG590 3.7 25.0 1.0
CB A:SER684 3.7 24.9 1.0
N A:SER684 3.9 25.5 1.0
C A:VAL683 4.0 26.4 1.0
O A:VAL683 4.0 26.3 1.0
CB A:VAL683 4.1 27.3 1.0
C27 A:9HI2 4.1 43.8 1.0
CG A:ARG590 4.2 26.2 1.0
CA A:SER684 4.3 24.9 1.0
O A:HOH993 4.5 55.5 1.0
O A:HOH976 4.6 42.7 1.0
CA A:VAL683 4.7 27.0 1.0
CB A:SER661 4.7 37.2 1.0
OG A:SER684 4.9 24.8 1.0
CD2 B:LEU857 5.0 32.5 1.0

Fluorine binding site 5 out of 8 in 3cdb

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Fluorine binding site 5 out of 8 in the Thermodynamic and Structure Guided Design of Statin Hmg-Coa Reductase Inhibitors


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Thermodynamic and Structure Guided Design of Statin Hmg-Coa Reductase Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F4

b:48.1
occ:1.00
 F2 C:9HI4 0.0 48.1 1.0
C28 C:9HI4 1.3 48.7 1.0
C22 C:9HI4 2.4 48.3 1.0
C19 C:9HI4 2.4 49.0 1.0
O D:HIS861 2.9 48.4 1.0
CB D:HIS861 3.1 48.2 1.0
C D:HIS861 3.1 48.1 1.0
N D:HIS861 3.1 47.3 1.0
CA D:HIS861 3.2 47.9 1.0
CG D:HIS861 3.6 49.2 1.0
C25 C:9HI4 3.6 47.7 1.0
C16 C:9HI4 3.6 48.3 1.0
CD2 D:HIS861 3.7 49.8 1.0
O D:ALA856 3.7 34.9 1.0
C31 C:9HI4 4.1 47.2 1.0
C D:GLY860 4.2 46.5 1.0
O D:HOH893 4.3 29.2 1.0
C D:ALA856 4.5 34.5 1.0
ND1 D:HIS861 4.7 50.5 1.0
CA D:GLY860 4.8 45.6 1.0
NE2 D:HIS861 4.8 50.4 1.0
CA D:LEU857 4.9 35.9 1.0
CG1 C:VAL683 4.9 29.7 1.0

Fluorine binding site 6 out of 8 in 3cdb

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Fluorine binding site 6 out of 8 in the Thermodynamic and Structure Guided Design of Statin Hmg-Coa Reductase Inhibitors


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Thermodynamic and Structure Guided Design of Statin Hmg-Coa Reductase Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F4

b:45.7
occ:1.00
 F1 C:9HI4 0.0 45.7 1.0
C30 C:9HI4 1.3 45.6 1.0
C24 C:9HI4 2.4 45.5 1.0
C15 C:9HI4 2.4 45.4 1.0
NE C:ARG590 2.7 34.0 1.0
CZ C:ARG590 3.1 34.5 1.0
CG1 C:VAL683 3.3 29.7 1.0
CD C:ARG590 3.3 33.3 1.0
NH2 C:ARG590 3.4 34.7 1.0
C21 C:9HI4 3.6 44.9 1.0
C18 C:9HI4 3.6 45.2 1.0
NH1 C:ARG590 3.8 34.4 1.0
CB C:SER684 3.9 26.5 1.0
O C:VAL683 4.0 28.6 1.0
C C:VAL683 4.0 28.5 1.0
CG2 C:VAL683 4.1 29.7 1.0
CG C:ARG590 4.1 31.8 1.0
N C:SER684 4.1 27.4 1.0
C27 C:9HI4 4.1 44.9 1.0
CB C:VAL683 4.2 29.4 1.0
O C:HOH989 4.3 51.0 1.0
CA C:SER684 4.5 26.5 1.0
CB C:SER661 4.5 45.5 1.0
CA C:VAL683 4.7 29.3 1.0

Fluorine binding site 7 out of 8 in 3cdb

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Fluorine binding site 7 out of 8 in the Thermodynamic and Structure Guided Design of Statin Hmg-Coa Reductase Inhibitors


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Thermodynamic and Structure Guided Design of Statin Hmg-Coa Reductase Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F3

b:46.4
occ:1.00
 F2 D:9HI3 0.0 46.4 1.0
C28 D:9HI3 1.3 46.9 1.0
C19 D:9HI3 2.4 46.7 1.0
C22 D:9HI3 2.4 46.9 1.0
O C:GLY860 3.2 38.1 1.0
C C:HIS861 3.3 38.0 1.0
O C:ALA856 3.6 31.9 1.0
C16 D:9HI3 3.6 46.6 1.0
C25 D:9HI3 3.7 46.1 1.0
C C:GLY860 3.7 37.8 1.0
O C:HIS861 3.9 38.5 1.0
C31 D:9HI3 4.1 45.5 1.0
N C:HIS861 4.2 37.9 1.0
CA C:HIS861 4.4 37.7 1.0
CA C:GLY860 4.4 37.5 1.0
C C:ALA856 4.4 31.5 1.0
O C:HOH891 4.7 23.1 1.0
N C:GLY860 4.8 37.2 1.0

Fluorine binding site 8 out of 8 in 3cdb

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Fluorine binding site 8 out of 8 in the Thermodynamic and Structure Guided Design of Statin Hmg-Coa Reductase Inhibitors


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Thermodynamic and Structure Guided Design of Statin Hmg-Coa Reductase Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F3

b:45.0
occ:1.00
 F1 D:9HI3 0.0 45.0 1.0
C30 D:9HI3 1.3 44.5 1.0
C24 D:9HI3 2.4 44.1 1.0
C15 D:9HI3 2.4 44.4 1.0
NE D:ARG590 2.8 29.0 1.0
CZ D:ARG590 3.1 29.3 1.0
CG1 D:VAL683 3.2 27.3 1.0
CD D:ARG590 3.3 28.3 1.0
NH2 D:ARG590 3.4 28.9 1.0
C21 D:9HI3 3.6 44.1 1.0
C18 D:9HI3 3.6 44.3 1.0
NH1 D:ARG590 3.8 29.6 1.0
CG2 D:VAL683 3.8 28.4 1.0
CB D:SER661 4.0 36.4 1.0
CB D:VAL683 4.1 27.7 1.0
CG D:ARG590 4.1 27.3 1.0
C D:VAL683 4.1 27.0 1.0
O D:VAL683 4.1 27.2 1.0
CB D:SER684 4.1 25.6 1.0
C27 D:9HI3 4.1 43.9 1.0
N D:SER684 4.2 26.1 1.0
O D:HOH1011 4.3 49.4 1.0
CA D:SER684 4.6 25.6 1.0
CA D:VAL683 4.7 27.6 1.0
CE D:MET657 4.8 41.7 1.0

Reference:

R.W.Sarver, E.Bills, G.Bolton, L.D.Bratton, N.L.Caspers, J.B.Dunbar, M.S.Harris, R.H.Hutchings, R.M.Kennedy, S.D.Larsen, A.Pavlovsky, J.A.Pfefferkorn, G.Bainbridge. Thermodynamic and Structure Guided Design of Statin Based Inhibitors of 3-Hydroxy-3-Methylglutaryl Coenzyme A Reductase. J.Med.Chem. V. 51 3804 2008.
ISSN: ISSN 0022-2623
PubMed: 18540668
DOI: 10.1021/JM7015057
Page generated: Wed Jul 31 17:26:21 2024

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