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Calcium in PDB 3uy9: Bovine Trypsin Variant X(TRIPLEGLU217PHE227) in Complex with Small Molecule Inhibitor

Enzymatic activity of Bovine Trypsin Variant X(TRIPLEGLU217PHE227) in Complex with Small Molecule Inhibitor

All present enzymatic activity of Bovine Trypsin Variant X(TRIPLEGLU217PHE227) in Complex with Small Molecule Inhibitor:
3.4.21.4;

Protein crystallography data

The structure of Bovine Trypsin Variant X(TRIPLEGLU217PHE227) in Complex with Small Molecule Inhibitor, PDB code: 3uy9 was solved by A.Tziridis, P.Neumann, P.Kolenko, M.T.Stubbs, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 120.78 / 3.22
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 88.069, 98.569, 120.781, 89.62, 88.85, 103.99
R / Rfree (%) 20.5 / 26.1

Other elements in 3uy9:

The structure of Bovine Trypsin Variant X(TRIPLEGLU217PHE227) in Complex with Small Molecule Inhibitor also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Calcium atom in the Bovine Trypsin Variant X(TRIPLEGLU217PHE227) in Complex with Small Molecule Inhibitor (pdb code 3uy9). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 16 binding sites of Calcium where determined in the Bovine Trypsin Variant X(TRIPLEGLU217PHE227) in Complex with Small Molecule Inhibitor, PDB code: 3uy9:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 16 in 3uy9

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Calcium binding site 1 out of 16 in the Bovine Trypsin Variant X(TRIPLEGLU217PHE227) in Complex with Small Molecule Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Bovine Trypsin Variant X(TRIPLEGLU217PHE227) in Complex with Small Molecule Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca480

b:30.0
occ:1.00
 OE2 A:GLU80 2.0 33.4 1.0
OE1 A:GLU70 2.1 35.0 1.0
O A:VAL75 2.1 37.0 1.0
O A:ASN72 2.4 34.3 1.0
CD A:GLU80 3.0 35.6 1.0
CD A:GLU70 3.3 34.8 1.0
C A:VAL75 3.3 37.1 1.0
CG A:GLU80 3.5 34.8 1.0
C A:ASN72 3.6 34.3 1.0
OE1 A:GLU77 3.7 39.9 1.0
OE2 A:GLU70 3.9 35.5 1.0
CA A:VAL76 4.0 36.6 1.0
N A:GLU77 4.0 36.6 1.0
OE1 A:GLU80 4.0 34.4 1.0
N A:VAL76 4.1 36.8 1.0
N A:VAL75 4.1 37.6 1.0
CA A:ILE73 4.3 35.1 1.0
CA A:VAL75 4.3 37.1 1.0
N A:ILE73 4.4 34.7 1.0
C A:ILE73 4.4 35.8 1.0
CG A:GLU70 4.5 32.1 1.0
C A:VAL76 4.5 36.6 1.0
CG A:GLU77 4.5 38.0 1.0
CD A:GLU77 4.6 39.9 1.0
CA A:ASN72 4.6 34.1 1.0
N A:ASN72 4.6 33.6 1.0
O A:ILE73 4.6 35.9 1.0
CB A:GLU77 4.8 36.7 1.0
CB A:GLU70 4.8 31.8 1.0
N A:ASP71 4.8 32.9 1.0
CA A:GLU70 4.8 32.1 1.0
CB A:ASN72 4.9 34.1 1.0
N A:ASN74 5.0 36.7 1.0

Calcium binding site 2 out of 16 in 3uy9

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Calcium binding site 2 out of 16 in the Bovine Trypsin Variant X(TRIPLEGLU217PHE227) in Complex with Small Molecule Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Bovine Trypsin Variant X(TRIPLEGLU217PHE227) in Complex with Small Molecule Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca480

b:30.0
occ:1.00
 OE1 B:GLU70 2.1 35.0 1.0
O B:VAL75 2.1 37.0 1.0
O B:ASN72 2.4 34.4 1.0
OE2 B:GLU80 2.4 33.5 1.0
CD B:GLU70 3.1 35.0 1.0
C B:VAL75 3.2 37.0 1.0
CD B:GLU80 3.3 35.6 1.0
OE2 B:GLU70 3.5 35.6 1.0
C B:ASN72 3.5 34.4 1.0
CG B:GLU80 3.6 34.8 1.0
CA B:VAL76 3.9 36.5 1.0
OE1 B:GLU77 3.9 40.0 1.0
N B:VAL75 3.9 37.4 1.0
N B:VAL76 4.0 36.6 1.0
CA B:ILE73 4.1 35.1 1.0
C B:ILE73 4.2 35.7 1.0
N B:GLU77 4.2 36.5 1.0
CA B:VAL75 4.2 37.1 1.0
OE1 B:GLU80 4.3 34.4 1.0
N B:ILE73 4.3 34.5 1.0
O B:ILE73 4.3 35.8 1.0
CG B:GLU70 4.5 32.3 1.0
C B:VAL76 4.5 36.6 1.0
CA B:ASN72 4.6 34.1 1.0
N B:ASN74 4.7 36.5 1.0
CG B:GLU77 4.7 38.0 1.0
N B:ASN72 4.8 33.9 1.0
CD B:GLU77 4.8 40.0 1.0
CB B:GLU70 4.9 31.8 1.0
CB B:ASN72 5.0 34.0 1.0

Calcium binding site 3 out of 16 in 3uy9

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Calcium binding site 3 out of 16 in the Bovine Trypsin Variant X(TRIPLEGLU217PHE227) in Complex with Small Molecule Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Bovine Trypsin Variant X(TRIPLEGLU217PHE227) in Complex with Small Molecule Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca480

b:30.0
occ:1.00
 OE2 C:GLU80 2.0 33.2 1.0
OE1 C:GLU70 2.1 35.1 1.0
O C:VAL75 2.4 37.0 1.0
O C:ASN72 2.4 34.3 1.0
CD C:GLU80 3.1 35.5 1.0
CD C:GLU70 3.3 34.9 1.0
C C:VAL75 3.4 37.1 1.0
C C:ASN72 3.5 34.2 1.0
CG C:GLU80 3.6 35.0 1.0
OE1 C:GLU77 3.8 40.0 1.0
OE2 C:GLU70 3.9 35.8 1.0
CA C:VAL76 4.0 36.6 1.0
N C:GLU77 4.1 36.5 1.0
N C:VAL76 4.2 36.8 1.0
OE1 C:GLU80 4.2 33.9 1.0
N C:VAL75 4.2 37.5 1.0
CA C:ILE73 4.3 35.1 1.0
N C:ILE73 4.4 34.3 1.0
CA C:VAL75 4.4 37.1 1.0
CG C:GLU70 4.4 32.0 1.0
N C:ASN72 4.4 33.5 1.0
CA C:ASN72 4.5 34.0 1.0
C C:ILE73 4.5 35.8 1.0
C C:VAL76 4.5 36.5 1.0
CG C:GLU77 4.5 37.7 1.0
CD C:GLU77 4.6 39.6 1.0
CB C:GLU70 4.7 31.7 1.0
O C:ILE73 4.7 35.9 1.0
N C:ASP71 4.7 33.0 1.0
CA C:GLU70 4.8 32.1 1.0
CB C:GLU77 4.8 36.6 1.0
CB C:ASN72 4.8 34.0 1.0
N C:ASN74 5.0 36.4 1.0

Calcium binding site 4 out of 16 in 3uy9

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Calcium binding site 4 out of 16 in the Bovine Trypsin Variant X(TRIPLEGLU217PHE227) in Complex with Small Molecule Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Bovine Trypsin Variant X(TRIPLEGLU217PHE227) in Complex with Small Molecule Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca480

b:30.0
occ:1.00
 OE2 D:GLU80 2.1 33.4 1.0
OE1 D:GLU70 2.1 35.0 1.0
O D:ASN72 2.2 34.4 1.0
O D:VAL75 2.3 37.0 1.0
CD D:GLU80 3.2 35.5 1.0
CD D:GLU70 3.3 34.9 1.0
C D:VAL75 3.4 37.2 1.0
C D:ASN72 3.4 34.3 1.0
CG D:GLU80 3.7 34.7 1.0
OE1 D:GLU77 3.8 40.1 1.0
OE2 D:GLU70 3.8 35.9 1.0
N D:GLU77 4.1 36.5 1.0
N D:VAL75 4.2 37.3 1.0
CA D:VAL76 4.2 36.5 1.0
OE1 D:GLU80 4.2 34.0 1.0
CA D:ILE73 4.2 34.9 1.0
N D:VAL76 4.3 36.8 1.0
N D:ILE73 4.3 34.5 1.0
CA D:VAL75 4.4 37.1 1.0
N D:ASN72 4.4 33.7 1.0
CA D:ASN72 4.4 33.9 1.0
CG D:GLU70 4.5 32.0 1.0
C D:ILE73 4.5 35.6 1.0
N D:ASP71 4.6 32.8 1.0
CG D:GLU77 4.6 37.7 1.0
CD D:GLU77 4.6 39.6 1.0
CA D:GLU70 4.7 32.0 1.0
CB D:GLU70 4.7 31.6 1.0
C D:VAL76 4.7 36.6 1.0
CB D:ASN72 4.7 33.9 1.0
O D:ILE73 4.7 35.7 1.0
CB D:GLU77 4.8 36.6 1.0
N D:ASN74 5.0 36.4 1.0

Calcium binding site 5 out of 16 in 3uy9

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Calcium binding site 5 out of 16 in the Bovine Trypsin Variant X(TRIPLEGLU217PHE227) in Complex with Small Molecule Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Bovine Trypsin Variant X(TRIPLEGLU217PHE227) in Complex with Small Molecule Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca480

b:30.0
occ:1.00
 OE2 E:GLU80 1.9 33.2 1.0
OE1 E:GLU70 2.1 35.1 1.0
O E:VAL75 2.5 37.1 1.0
O E:ASN72 2.6 34.2 1.0
CD E:GLU80 2.7 35.7 1.0
CD E:GLU70 3.2 35.0 1.0
CG E:GLU80 3.3 34.9 1.0
C E:VAL75 3.4 37.1 1.0
C E:ASN72 3.7 34.4 1.0
OE1 E:GLU80 3.7 34.5 1.0
OE2 E:GLU70 3.8 35.7 1.0
OE1 E:GLU77 3.8 39.8 1.0
CA E:VAL76 3.9 36.5 1.0
N E:GLU77 3.9 36.5 1.0
N E:VAL76 4.1 36.7 1.0
N E:VAL75 4.2 37.4 1.0
CG E:GLU70 4.4 32.5 1.0
CA E:VAL75 4.4 37.1 1.0
CA E:ILE73 4.4 35.2 1.0
C E:VAL76 4.4 36.5 1.0
N E:ILE73 4.5 34.7 1.0
C E:ILE73 4.6 35.7 1.0
CG E:GLU77 4.7 37.9 1.0
CA E:ASN72 4.7 34.1 1.0
CB E:GLU80 4.7 34.2 1.0
CD E:GLU77 4.7 39.8 1.0
O E:ILE73 4.7 35.8 1.0
N E:ASN72 4.8 33.6 1.0
CB E:GLU70 4.8 31.7 1.0
CA E:GLU70 4.9 32.1 1.0
CB E:GLU77 4.9 36.6 1.0

Calcium binding site 6 out of 16 in 3uy9

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Calcium binding site 6 out of 16 in the Bovine Trypsin Variant X(TRIPLEGLU217PHE227) in Complex with Small Molecule Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Bovine Trypsin Variant X(TRIPLEGLU217PHE227) in Complex with Small Molecule Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca480

b:30.0
occ:1.00
 OE2 F:GLU80 2.0 33.4 1.0
OE1 F:GLU70 2.1 34.8 1.0
O F:VAL75 2.2 37.0 1.0
O F:ASN72 2.3 34.4 1.0
CD F:GLU80 3.2 35.6 1.0
CD F:GLU70 3.3 34.7 1.0
C F:VAL75 3.5 37.1 1.0
C F:ASN72 3.5 34.2 1.0
CG F:GLU80 3.6 34.8 1.0
OE1 F:GLU77 3.7 40.2 1.0
OE2 F:GLU70 3.9 35.3 1.0
N F:GLU77 4.0 36.5 1.0
CA F:VAL76 4.1 36.5 1.0
CA F:ILE73 4.2 35.0 1.0
N F:VAL75 4.2 37.4 1.0
N F:VAL76 4.3 36.7 1.0
N F:ILE73 4.3 34.2 1.0
OE1 F:GLU80 4.3 34.1 1.0
CG F:GLU70 4.4 32.3 1.0
CA F:VAL75 4.4 37.1 1.0
C F:ILE73 4.5 35.7 1.0
N F:ASN72 4.5 33.5 1.0
CA F:ASN72 4.5 33.9 1.0
CG F:GLU77 4.5 37.7 1.0
CD F:GLU77 4.5 39.6 1.0
N F:ASP71 4.6 32.9 1.0
C F:VAL76 4.6 36.6 1.0
CB F:GLU70 4.7 31.6 1.0
O F:ILE73 4.7 35.9 1.0
CA F:GLU70 4.7 32.0 1.0
CB F:GLU77 4.8 36.5 1.0
CB F:ASN72 4.9 33.9 1.0
N F:ASN74 5.0 36.5 1.0

Calcium binding site 7 out of 16 in 3uy9

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Calcium binding site 7 out of 16 in the Bovine Trypsin Variant X(TRIPLEGLU217PHE227) in Complex with Small Molecule Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Bovine Trypsin Variant X(TRIPLEGLU217PHE227) in Complex with Small Molecule Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca480

b:30.0
occ:1.00
 OE1 G:GLU70 2.0 35.0 1.0
O G:ASN72 2.2 34.1 1.0
OE2 G:GLU80 2.3 33.5 1.0
O G:VAL75 2.4 37.0 1.0
CD G:GLU70 3.2 34.9 1.0
CD G:GLU80 3.3 35.5 1.0
C G:ASN72 3.4 34.0 1.0
C G:VAL75 3.5 37.0 1.0
CG G:GLU80 3.7 34.8 1.0
OE1 G:GLU77 3.8 39.8 1.0
OE2 G:GLU70 3.8 35.6 1.0
N G:VAL75 4.1 37.5 1.0
CA G:ILE73 4.1 35.1 1.0
N G:ILE73 4.2 34.2 1.0
C G:ILE73 4.2 35.6 1.0
N G:ASN72 4.3 33.7 1.0
CA G:ASN72 4.3 34.0 1.0
N G:GLU77 4.3 36.5 1.0
CA G:VAL76 4.3 36.5 1.0
OE1 G:GLU80 4.3 33.9 1.0
O G:ILE73 4.3 35.6 1.0
CA G:VAL75 4.3 37.1 1.0
CG G:GLU70 4.4 32.3 1.0
N G:VAL76 4.4 36.6 1.0
CB G:GLU70 4.6 31.5 1.0
N G:ASP71 4.6 32.9 1.0
CD G:GLU77 4.6 39.6 1.0
CB G:ASN72 4.7 34.0 1.0
CG G:GLU77 4.7 37.7 1.0
CA G:GLU70 4.7 32.0 1.0
N G:ASN74 4.8 36.3 1.0
C G:VAL76 4.8 36.6 1.0
CB G:GLU77 5.0 36.6 1.0

Calcium binding site 8 out of 16 in 3uy9

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Calcium binding site 8 out of 16 in the Bovine Trypsin Variant X(TRIPLEGLU217PHE227) in Complex with Small Molecule Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Bovine Trypsin Variant X(TRIPLEGLU217PHE227) in Complex with Small Molecule Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca480

b:30.0
occ:1.00
 OE2 H:GLU80 2.0 33.3 1.0
OE1 H:GLU70 2.0 35.0 1.0
O H:VAL75 2.3 37.1 1.0
O H:ASN72 2.5 34.4 1.0
CD H:GLU80 2.8 35.6 1.0
CD H:GLU70 3.2 34.9 1.0
CG H:GLU80 3.4 34.9 1.0
C H:VAL75 3.5 37.1 1.0
OE1 H:GLU77 3.6 39.9 1.0
C H:ASN72 3.6 34.5 1.0
OE2 H:GLU70 3.8 35.7 1.0
OE1 H:GLU80 3.8 34.2 1.0
N H:GLU77 4.0 36.5 1.0
CA H:VAL76 4.1 36.5 1.0
N H:VAL76 4.2 36.6 1.0
CG H:GLU70 4.3 32.5 1.0
N H:VAL75 4.3 37.5 1.0
CA H:ILE73 4.3 35.1 1.0
N H:ILE73 4.4 34.6 1.0
CA H:VAL75 4.5 37.1 1.0
C H:VAL76 4.6 36.5 1.0
CD H:GLU77 4.6 40.0 1.0
C H:ILE73 4.6 35.7 1.0
CG H:GLU77 4.6 38.0 1.0
CA H:ASN72 4.6 34.1 1.0
N H:ASN72 4.7 33.8 1.0
CB H:GLU70 4.7 31.8 1.0
CA H:GLU70 4.8 32.0 1.0
N H:ASP71 4.8 32.8 1.0
CB H:GLU77 4.8 36.6 1.0
O H:ILE73 4.9 35.6 1.0
CB H:GLU80 4.9 34.2 1.0

Calcium binding site 9 out of 16 in 3uy9

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Calcium binding site 9 out of 16 in the Bovine Trypsin Variant X(TRIPLEGLU217PHE227) in Complex with Small Molecule Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Bovine Trypsin Variant X(TRIPLEGLU217PHE227) in Complex with Small Molecule Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca480

b:30.0
occ:1.00
 OE1 I:GLU70 2.1 35.0 1.0
OE2 I:GLU80 2.2 33.4 1.0
O I:VAL75 2.2 37.2 1.0
O I:ASN72 2.6 34.4 1.0
CD I:GLU80 2.8 35.6 1.0
CD I:GLU70 3.2 34.9 1.0
CG I:GLU80 3.2 34.9 1.0
C I:VAL75 3.4 37.2 1.0
OE1 I:GLU80 3.7 34.2 1.0
OE2 I:GLU70 3.8 36.0 1.0
C I:ASN72 3.8 34.4 1.0
CA I:VAL76 3.9 36.6 1.0
OE1 I:GLU77 4.0 40.1 1.0
N I:GLU77 4.0 36.4 1.0
N I:VAL76 4.1 36.8 1.0
CG I:GLU70 4.3 32.3 1.0
N I:VAL75 4.3 37.5 1.0
C I:VAL76 4.5 36.5 1.0
CA I:ILE73 4.5 35.2 1.0
CA I:VAL75 4.5 37.2 1.0
CG I:GLU77 4.6 38.1 1.0
N I:ILE73 4.6 34.6 1.0
C I:ILE73 4.7 35.9 1.0
CB I:GLU80 4.7 34.2 1.0
CB I:GLU70 4.7 31.9 1.0
CB I:GLU77 4.8 36.9 1.0
CD I:GLU77 4.8 39.7 1.0
CA I:GLU70 4.8 32.1 1.0
O I:ILE73 4.8 35.9 1.0
N I:ASN72 4.8 33.6 1.0
CA I:ASN72 4.9 34.0 1.0
N I:ASP71 4.9 33.0 1.0
CA I:GLU77 5.0 36.7 1.0

Calcium binding site 10 out of 16 in 3uy9

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Calcium binding site 10 out of 16 in the Bovine Trypsin Variant X(TRIPLEGLU217PHE227) in Complex with Small Molecule Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Bovine Trypsin Variant X(TRIPLEGLU217PHE227) in Complex with Small Molecule Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Ca480

b:30.0
occ:1.00
 OE1 J:GLU70 2.1 35.0 1.0
OE2 J:GLU80 2.1 33.5 1.0
O J:VAL75 2.2 36.9 1.0
O J:ASN72 2.4 34.5 1.0
CD J:GLU80 3.1 35.7 1.0
CD J:GLU70 3.1 34.8 1.0
C J:VAL75 3.5 37.1 1.0
C J:ASN72 3.5 34.4 1.0
CG J:GLU80 3.6 34.7 1.0
OE2 J:GLU70 3.7 35.8 1.0
OE1 J:GLU77 3.8 39.9 1.0
OE1 J:GLU80 4.1 34.6 1.0
CA J:VAL76 4.2 36.6 1.0
N J:GLU77 4.2 36.4 1.0
CA J:ILE73 4.3 35.2 1.0
N J:VAL76 4.3 36.8 1.0
N J:VAL75 4.3 37.6 1.0
N J:ILE73 4.3 34.7 1.0
CG J:GLU70 4.3 32.4 1.0
N J:ASN72 4.4 33.5 1.0
CA J:ASN72 4.5 33.9 1.0
CA J:VAL75 4.5 37.2 1.0
C J:ILE73 4.5 35.6 1.0
CG J:GLU77 4.5 38.0 1.0
CD J:GLU77 4.6 39.8 1.0
N J:ASP71 4.6 33.0 1.0
CB J:GLU70 4.7 32.0 1.0
C J:VAL76 4.7 36.6 1.0
CA J:GLU70 4.7 32.1 1.0
CB J:GLU77 4.8 36.9 1.0
O J:ILE73 4.8 35.8 1.0
CB J:ASN72 4.9 34.0 1.0

Reference:

A.Tziridis, D.Rauh, P.Neumann, P.Kolenko, A.Menzel, U.Brauer, C.Ursel, P.Steinmetzer, J.Sturzebecher, A.Schweinitz, T.Steinmetzer, M.T.Stubbs. Correlating Structure and Ligand Affinity in Drug Discovery: A Cautionary Tale Involving Second Shell Residues. Biol.Chem. V. 395 891 2014.
ISSN: ISSN 1431-6730
PubMed: 25003390
DOI: 10.1515/HSZ-2014-0158
Page generated: Sat Jul 13 20:21:52 2024

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