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Fluorine in PDB 3lgp: Crystal Structure of Catalytic Domain of Tace with Benzimidazolyl- Thienyl-Tartrate Based Inhibitor

Enzymatic activity of Crystal Structure of Catalytic Domain of Tace with Benzimidazolyl- Thienyl-Tartrate Based Inhibitor

All present enzymatic activity of Crystal Structure of Catalytic Domain of Tace with Benzimidazolyl- Thienyl-Tartrate Based Inhibitor:
3.4.24.86;

Protein crystallography data

The structure of Crystal Structure of Catalytic Domain of Tace with Benzimidazolyl- Thienyl-Tartrate Based Inhibitor, PDB code: 3lgp was solved by P.Orth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.16 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 73.344, 76.618, 103.506, 90.00, 90.00, 90.00
R / Rfree (%) 20.1 / 24.4

Other elements in 3lgp:

The structure of Crystal Structure of Catalytic Domain of Tace with Benzimidazolyl- Thienyl-Tartrate Based Inhibitor also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Zinc (Zn) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Catalytic Domain of Tace with Benzimidazolyl- Thienyl-Tartrate Based Inhibitor (pdb code 3lgp). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of Catalytic Domain of Tace with Benzimidazolyl- Thienyl-Tartrate Based Inhibitor, PDB code: 3lgp:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 3lgp

Go back to Fluorine Binding Sites List in 3lgp
Fluorine binding site 1 out of 6 in the Crystal Structure of Catalytic Domain of Tace with Benzimidazolyl- Thienyl-Tartrate Based 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 Catalytic Domain of Tace with Benzimidazolyl- Thienyl-Tartrate Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F485

b:45.5
occ:1.00
 F32 A:50X485 0.0 45.5 1.0
C31 A:50X485 1.3 45.5 1.0
F34 A:50X485 2.2 43.3 1.0
F33 A:50X485 2.2 46.0 1.0
C13 A:50X485 2.3 42.5 1.0
N14 A:50X485 2.7 41.1 1.0
CG2 A:VAL440 2.8 56.6 1.0
N12 A:50X485 3.7 40.3 1.0
N A:VAL440 3.8 49.4 1.0
N A:SER441 3.8 52.0 1.0
OG A:SER441 3.9 66.0 1.0
ND2 A:ASN447 3.9 37.4 1.0
O A:ILE438 3.9 39.1 1.0
C7 A:50X485 4.0 42.0 1.0
CB A:LYS432 4.1 32.8 1.0
CB A:VAL440 4.1 56.6 1.0
CG A:ASN447 4.1 46.3 1.0
CA A:VAL440 4.3 51.3 1.0
C30 A:50X485 4.4 38.7 1.0
O A:HOH537 4.5 41.0 1.0
O A:TYR433 4.5 29.1 1.0
OD1 A:ASN447 4.5 39.5 1.0
C6 A:50X485 4.5 40.4 1.0
C A:VAL440 4.6 55.6 1.0
C A:ALA439 4.6 48.8 1.0
CB A:ASN447 4.6 32.6 1.0
CB A:TYR436 4.7 30.6 1.0
CA A:SER441 4.7 52.3 1.0
CA A:ALA439 4.7 40.1 1.0
O A:LYS432 4.7 32.7 1.0
CB A:SER441 4.7 57.5 1.0
N A:GLY442 4.8 51.6 1.0
CG A:LYS432 4.8 34.7 1.0
C A:LYS432 4.9 32.6 1.0
CA A:ASN447 4.9 31.6 1.0
C A:ILE438 5.0 40.5 1.0
CA A:LYS432 5.0 30.3 1.0

Fluorine binding site 2 out of 6 in 3lgp

Go back to Fluorine Binding Sites List in 3lgp
Fluorine binding site 2 out of 6 in the Crystal Structure of Catalytic Domain of Tace with Benzimidazolyl- Thienyl-Tartrate Based 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 Catalytic Domain of Tace with Benzimidazolyl- Thienyl-Tartrate Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F485

b:46.0
occ:1.00
 F33 A:50X485 0.0 46.0 1.0
C31 A:50X485 1.4 45.5 1.0
F32 A:50X485 2.2 45.5 1.0
F34 A:50X485 2.3 43.3 1.0
C13 A:50X485 2.5 42.5 1.0
N12 A:50X485 3.1 40.3 1.0
C30 A:50X485 3.1 38.7 1.0
C18 A:50X485 3.2 39.4 1.0
O A:ILE438 3.3 39.1 1.0
O A:TYR433 3.4 29.1 1.0
CB A:TYR436 3.5 30.6 1.0
C17 A:50X485 3.5 40.0 1.0
N14 A:50X485 3.6 41.1 1.0
O A:VAL434 3.9 28.4 1.0
O A:TYR436 4.0 30.7 1.0
N A:TYR436 4.2 29.1 1.0
CG2 A:VAL440 4.2 56.6 1.0
CA A:TYR436 4.2 29.6 1.0
C A:ILE438 4.3 40.5 1.0
C A:VAL434 4.3 29.3 1.0
C6 A:50X485 4.4 40.4 1.0
C A:TYR436 4.4 33.1 1.0
C A:TYR433 4.4 30.2 1.0
CA A:VAL434 4.4 25.2 1.0
CA A:ALA439 4.4 40.1 1.0
N A:VAL440 4.5 49.4 1.0
C7 A:50X485 4.5 42.0 1.0
CG A:TYR436 4.6 31.8 1.0
C19 A:50X485 4.6 35.0 1.0
CB A:LYS432 4.6 32.8 1.0
CD2 A:TYR436 4.7 32.6 1.0
N A:ALA439 4.8 39.0 1.0
N A:VAL434 4.9 25.7 1.0

Fluorine binding site 3 out of 6 in 3lgp

Go back to Fluorine Binding Sites List in 3lgp
Fluorine binding site 3 out of 6 in the Crystal Structure of Catalytic Domain of Tace with Benzimidazolyl- Thienyl-Tartrate Based 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 Catalytic Domain of Tace with Benzimidazolyl- Thienyl-Tartrate Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F485

b:43.3
occ:1.00
 F34 A:50X485 0.0 43.3 1.0
C31 A:50X485 1.4 45.5 1.0
F32 A:50X485 2.2 45.5 1.0
F33 A:50X485 2.3 46.0 1.0
C13 A:50X485 2.4 42.5 1.0
N12 A:50X485 3.2 40.3 1.0
N14 A:50X485 3.3 41.1 1.0
O A:ASN447 3.4 34.2 1.0
CA A:ASN447 3.4 31.6 1.0
C30 A:50X485 3.4 38.7 1.0
CB A:ASN447 3.5 32.6 1.0
O A:TYR433 3.5 29.1 1.0
CG A:ASN447 3.7 46.3 1.0
ND2 A:ASN447 3.8 37.4 1.0
C A:ASN447 3.8 35.7 1.0
C A:TYR433 3.9 30.2 1.0
CA A:VAL434 4.0 25.2 1.0
O A:LYS432 4.1 32.7 1.0
N A:VAL434 4.1 25.7 1.0
C7 A:50X485 4.4 42.0 1.0
C6 A:50X485 4.4 40.4 1.0
OD1 A:ASN447 4.5 39.5 1.0
C A:LYS432 4.5 32.6 1.0
N A:ASN447 4.6 32.4 1.0
C17 A:50X485 4.6 40.0 1.0
O A:VAL434 4.6 28.4 1.0
C A:VAL434 4.7 29.3 1.0
CD1 A:LEU401 4.7 36.0 1.0
CA A:TYR433 4.8 27.5 1.0
CB A:LYS432 4.8 32.8 1.0
N A:TYR433 4.9 28.0 1.0
CB A:VAL434 4.9 27.0 1.0
C18 A:50X485 5.0 39.4 1.0
CG2 A:VAL440 5.0 56.6 1.0

Fluorine binding site 4 out of 6 in 3lgp

Go back to Fluorine Binding Sites List in 3lgp
Fluorine binding site 4 out of 6 in the Crystal Structure of Catalytic Domain of Tace with Benzimidazolyl- Thienyl-Tartrate Based 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 Catalytic Domain of Tace with Benzimidazolyl- Thienyl-Tartrate Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F485

b:39.9
occ:1.00
 F32 B:50X485 0.0 39.9 1.0
C31 B:50X485 1.4 36.8 1.0
F34 B:50X485 2.1 33.4 1.0
F33 B:50X485 2.2 36.7 1.0
C13 B:50X485 2.4 32.4 1.0
N14 B:50X485 2.9 31.7 1.0
N B:SER441 3.7 35.1 1.0
N12 B:50X485 3.7 30.3 1.0
ND2 B:ASN447 3.7 34.2 1.0
CB B:LYS432 3.8 30.6 1.0
OG B:SER441 3.8 52.4 1.0
CB B:SER441 3.8 37.9 1.0
CG B:ASN447 3.9 39.2 1.0
CG2 B:VAL440 4.0 40.0 1.0
N B:VAL440 4.2 33.6 1.0
OD1 B:ASN447 4.2 32.2 1.0
CA B:SER441 4.2 34.0 1.0
C7 B:50X485 4.3 30.1 1.0
CG B:LYS432 4.4 33.5 1.0
O B:ILE438 4.4 29.6 1.0
N B:GLY442 4.4 33.3 1.0
CB B:TYR436 4.5 27.7 1.0
C30 B:50X485 4.5 27.5 1.0
CB B:ASN447 4.5 28.6 1.0
O B:HOH487 4.5 39.0 1.0
O B:TYR433 4.6 28.0 1.0
C B:VAL440 4.7 39.1 1.0
O B:LYS432 4.7 32.5 1.0
C6 B:50X485 4.7 28.9 1.0
C B:SER441 4.7 35.9 1.0
CA B:VAL440 4.8 35.6 1.0
CA B:LYS432 4.8 28.4 1.0
C B:LYS432 4.8 32.8 1.0
CA B:ASN447 4.9 28.3 1.0
C B:ALA439 4.9 34.0 1.0
CG B:TYR436 5.0 28.7 1.0

Fluorine binding site 5 out of 6 in 3lgp

Go back to Fluorine Binding Sites List in 3lgp
Fluorine binding site 5 out of 6 in the Crystal Structure of Catalytic Domain of Tace with Benzimidazolyl- Thienyl-Tartrate Based 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 Catalytic Domain of Tace with Benzimidazolyl- Thienyl-Tartrate Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F485

b:36.7
occ:1.00
 F33 B:50X485 0.0 36.7 1.0
C31 B:50X485 1.4 36.8 1.0
F34 B:50X485 2.2 33.4 1.0
F32 B:50X485 2.2 39.9 1.0
C13 B:50X485 2.4 32.4 1.0
N12 B:50X485 3.0 30.3 1.0
C30 B:50X485 3.1 27.5 1.0
C18 B:50X485 3.2 27.9 1.0
CB B:TYR436 3.3 27.7 1.0
N14 B:50X485 3.5 31.7 1.0
O B:ILE438 3.5 29.6 1.0
C17 B:50X485 3.5 28.5 1.0
O B:TYR433 3.6 28.0 1.0
O B:VAL434 4.1 24.6 1.0
O B:TYR436 4.1 28.8 1.0
CA B:TYR436 4.2 26.9 1.0
N B:TYR436 4.2 26.1 1.0
CG B:TYR436 4.3 28.7 1.0
C6 B:50X485 4.3 28.9 1.0
CA B:ALA439 4.4 28.0 1.0
C B:TYR436 4.5 30.5 1.0
C B:ILE438 4.5 30.5 1.0
C7 B:50X485 4.5 30.1 1.0
C B:VAL434 4.5 25.6 1.0
CD2 B:TYR436 4.5 30.0 1.0
CB B:LYS432 4.6 30.6 1.0
C19 B:50X485 4.6 28.5 1.0
N B:VAL440 4.6 33.6 1.0
C B:TYR433 4.6 29.7 1.0
CA B:VAL434 4.7 24.1 1.0
N B:ALA439 4.9 27.5 1.0

Fluorine binding site 6 out of 6 in 3lgp

Go back to Fluorine Binding Sites List in 3lgp
Fluorine binding site 6 out of 6 in the Crystal Structure of Catalytic Domain of Tace with Benzimidazolyl- Thienyl-Tartrate Based 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 Catalytic Domain of Tace with Benzimidazolyl- Thienyl-Tartrate Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F485

b:33.4
occ:1.00
 F34 B:50X485 0.0 33.4 1.0
C31 B:50X485 1.3 36.8 1.0
F32 B:50X485 2.1 39.9 1.0
F33 B:50X485 2.2 36.7 1.0
C13 B:50X485 2.3 32.4 1.0
N12 B:50X485 3.1 30.3 1.0
C30 B:50X485 3.3 27.5 1.0
CB B:ASN447 3.4 28.6 1.0
N14 B:50X485 3.4 31.7 1.0
CA B:ASN447 3.5 28.3 1.0
O B:TYR433 3.5 28.0 1.0
O B:ASN447 3.6 31.6 1.0
CG B:ASN447 3.6 39.2 1.0
ND2 B:ASN447 3.7 34.2 1.0
C B:TYR433 4.0 29.7 1.0
C B:ASN447 4.0 33.1 1.0
CA B:VAL434 4.1 24.1 1.0
O B:LYS432 4.1 32.5 1.0
OD1 B:ASN447 4.3 32.2 1.0
N B:VAL434 4.3 25.0 1.0
C6 B:50X485 4.3 28.9 1.0
C7 B:50X485 4.4 30.1 1.0
C17 B:50X485 4.5 28.5 1.0
C B:LYS432 4.5 32.8 1.0
CB B:LYS432 4.5 30.6 1.0
O B:VAL434 4.6 24.6 1.0
C B:VAL434 4.7 25.6 1.0
N B:ASN447 4.7 26.7 1.0
C18 B:50X485 4.8 27.9 1.0
CB B:TYR436 4.8 27.7 1.0
N B:TYR433 4.9 29.6 1.0
CA B:TYR433 4.9 27.4 1.0
N B:GLY442 5.0 33.3 1.0

Reference:

D.Li, J.Popovici-Muller, D.B.Belanger, J.Caldwell, C.Dai, M.David, V.M.Girijavallabhan, B.J.Lavey, J.F.Lee, Z.Liu, R.Mazzola, R.Rizvi, K.E.Rosner, B.Shankar, J.Spitler, P.C.Ting, H.Vaccaro, W.Yu, G.Zhou, Z.Zhu, X.Niu, J.Sun, Z.Guo, P.Orth, S.Chen, J.A.Kozlowski, D.J.Lundell, V.Madison, B.Mckittrick, J.J.Piwinski, N.Y.Shih, G.W.Shipps, M.A.Siddiqui, C.O.Strickland. Structure and Activity Relationships of Tartrate-Based Tace Inhibitors. Bioorg.Med.Chem.Lett. V. 20 4812 2010.
ISSN: ISSN 0960-894X
PubMed: 20638281
DOI: 10.1016/J.BMCL.2010.06.104
Page generated: Wed Jul 31 20:29:42 2024

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