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Zinc in PDB 6f06: Cathepsin L in Complex with (3S,14E)-8-(Azetidin-3-Yl)-19-Chloro-N-(1- Cyanocyclopropyl)-5-Oxo-12,17-Dioxa-4-Azatricyclo[16.2.2.06, 11]Docosa-1(21),6,8,10,14,18(22),19-Heptaene-3-Carboxamide

Enzymatic activity of Cathepsin L in Complex with (3S,14E)-8-(Azetidin-3-Yl)-19-Chloro-N-(1- Cyanocyclopropyl)-5-Oxo-12,17-Dioxa-4-Azatricyclo[16.2.2.06, 11]Docosa-1(21),6,8,10,14,18(22),19-Heptaene-3-Carboxamide

All present enzymatic activity of Cathepsin L in Complex with (3S,14E)-8-(Azetidin-3-Yl)-19-Chloro-N-(1- Cyanocyclopropyl)-5-Oxo-12,17-Dioxa-4-Azatricyclo[16.2.2.06, 11]Docosa-1(21),6,8,10,14,18(22),19-Heptaene-3-Carboxamide:
3.4.22.15;

Protein crystallography data

The structure of Cathepsin L in Complex with (3S,14E)-8-(Azetidin-3-Yl)-19-Chloro-N-(1- Cyanocyclopropyl)-5-Oxo-12,17-Dioxa-4-Azatricyclo[16.2.2.06, 11]Docosa-1(21),6,8,10,14,18(22),19-Heptaene-3-Carboxamide, PDB code: 6f06 was solved by A.Kuglstatter, M.Stihle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.48 / 2.02
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 43.040, 50.791, 84.911, 90.00, 91.53, 90.00
R / Rfree (%) 20.1 / 27.4

Other elements in 6f06:

The structure of Cathepsin L in Complex with (3S,14E)-8-(Azetidin-3-Yl)-19-Chloro-N-(1- Cyanocyclopropyl)-5-Oxo-12,17-Dioxa-4-Azatricyclo[16.2.2.06, 11]Docosa-1(21),6,8,10,14,18(22),19-Heptaene-3-Carboxamide also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Zinc atom in the Cathepsin L in Complex with (3S,14E)-8-(Azetidin-3-Yl)-19-Chloro-N-(1- Cyanocyclopropyl)-5-Oxo-12,17-Dioxa-4-Azatricyclo[16.2.2.06, 11]Docosa-1(21),6,8,10,14,18(22),19-Heptaene-3-Carboxamide (pdb code 6f06). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 14 binding sites of Zinc where determined in the Cathepsin L in Complex with (3S,14E)-8-(Azetidin-3-Yl)-19-Chloro-N-(1- Cyanocyclopropyl)-5-Oxo-12,17-Dioxa-4-Azatricyclo[16.2.2.06, 11]Docosa-1(21),6,8,10,14,18(22),19-Heptaene-3-Carboxamide, PDB code: 6f06:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 14 in 6f06

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Zinc binding site 1 out of 14 in the Cathepsin L in Complex with (3S,14E)-8-(Azetidin-3-Yl)-19-Chloro-N-(1- Cyanocyclopropyl)-5-Oxo-12,17-Dioxa-4-Azatricyclo[16.2.2.06, 11]Docosa-1(21),6,8,10,14,18(22),19-Heptaene-3-Carboxamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cathepsin L in Complex with (3S,14E)-8-(Azetidin-3-Yl)-19-Chloro-N-(1- Cyanocyclopropyl)-5-Oxo-12,17-Dioxa-4-Azatricyclo[16.2.2.06, 11]Docosa-1(21),6,8,10,14,18(22),19-Heptaene-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:29.5
occ:1.00
 ND1 A:HIS163 1.9 24.0 1.0
O A:HOH402 2.1 23.6 1.0
SG A:CYS25 2.3 32.2 1.0
CL A:CL308 2.3 37.1 1.0
CE1 A:HIS163 2.8 24.4 1.0
CB A:CYS25 2.9 27.7 1.0
CG A:HIS163 3.0 23.9 1.0
N30 A:C7T301 3.2 36.6 1.0
CB A:HIS163 3.5 25.0 1.0
C29 A:C7T301 3.5 35.6 1.0
CA A:HIS163 3.6 27.1 1.0
O A:ASP162 4.0 30.3 1.0
NE2 A:HIS163 4.0 24.1 1.0
CD2 A:HIS163 4.1 22.1 1.0
CA A:CYS25 4.2 27.2 1.0
N A:GLY164 4.3 25.6 1.0
C2 A:C7T301 4.3 36.0 1.0
C A:HIS163 4.4 26.2 1.0
N16 A:C7T301 4.4 35.1 1.0
N A:CYS25 4.5 27.9 1.0
OE1 A:GLN19 4.6 26.3 1.0
N A:HIS163 4.7 27.2 1.0
NE2 A:GLN19 4.7 28.2 1.0
C A:ASP162 4.7 29.0 1.0

Zinc binding site 2 out of 14 in 6f06

Go back to Zinc Binding Sites List in 6f06
Zinc binding site 2 out of 14 in the Cathepsin L in Complex with (3S,14E)-8-(Azetidin-3-Yl)-19-Chloro-N-(1- Cyanocyclopropyl)-5-Oxo-12,17-Dioxa-4-Azatricyclo[16.2.2.06, 11]Docosa-1(21),6,8,10,14,18(22),19-Heptaene-3-Carboxamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cathepsin L in Complex with (3S,14E)-8-(Azetidin-3-Yl)-19-Chloro-N-(1- Cyanocyclopropyl)-5-Oxo-12,17-Dioxa-4-Azatricyclo[16.2.2.06, 11]Docosa-1(21),6,8,10,14,18(22),19-Heptaene-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:38.2
occ:1.00
 OD2 A:ASP137 1.9 33.0 1.0
NE2 A:HIS140 2.1 35.8 1.0
CG A:ASP137 2.7 31.6 1.0
OD1 A:ASP137 2.9 32.1 1.0
CE1 A:HIS140 2.9 36.7 1.0
CD2 A:HIS140 3.2 34.1 1.0
O A:ASP155 3.8 44.7 1.0
N A:SER157 3.8 36.9 1.0
ND1 A:HIS140 4.0 36.7 1.0
CB A:ASP137 4.2 29.8 1.0
CG A:HIS140 4.2 36.6 1.0
CA A:CYS156 4.2 38.0 1.0
CB A:SER157 4.3 43.6 1.0
C A:CYS156 4.4 37.3 1.0
CB A:ASP160 4.5 53.1 1.0
C A:ASP155 4.7 41.6 1.0
CA A:SER157 4.7 40.9 1.0
O A:ASP160 4.8 37.4 1.0
O A:GLY139 4.8 43.7 1.0
N A:CYS156 4.9 39.4 1.0
SG A:CYS156 5.0 31.9 1.0

Zinc binding site 3 out of 14 in 6f06

Go back to Zinc Binding Sites List in 6f06
Zinc binding site 3 out of 14 in the Cathepsin L in Complex with (3S,14E)-8-(Azetidin-3-Yl)-19-Chloro-N-(1- Cyanocyclopropyl)-5-Oxo-12,17-Dioxa-4-Azatricyclo[16.2.2.06, 11]Docosa-1(21),6,8,10,14,18(22),19-Heptaene-3-Carboxamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cathepsin L in Complex with (3S,14E)-8-(Azetidin-3-Yl)-19-Chloro-N-(1- Cyanocyclopropyl)-5-Oxo-12,17-Dioxa-4-Azatricyclo[16.2.2.06, 11]Docosa-1(21),6,8,10,14,18(22),19-Heptaene-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn304

b:28.3
occ:1.00
 OE2 A:GLU86 1.9 26.2 1.0
OE1 A:GLU50 1.9 18.1 1.0
O A:HOH434 1.9 34.7 1.0
O A:HOH447 2.1 10.8 1.0
CD A:GLU50 2.9 18.2 1.0
CD A:GLU86 2.9 27.3 1.0
OE2 A:GLU50 3.2 19.7 1.0
O A:LEU48 3.4 23.2 1.0
CG A:GLU86 3.7 27.3 1.0
OE1 A:GLU86 3.8 26.8 1.0
CB A:GLU86 4.0 25.3 1.0
O A:HOH417 4.0 21.2 1.0
O A:HOH409 4.1 32.2 1.0
CE2 A:PHE28 4.1 22.0 1.0
CG A:GLU50 4.2 18.6 1.0
CB A:TYR91 4.2 24.8 1.0
N A:GLU50 4.3 18.5 1.0
CD A:LYS17 4.5 35.0 1.0
C A:LEU48 4.5 23.1 1.0
CB A:GLU50 4.5 18.4 1.0
CZ A:PHE28 4.6 22.8 1.0
CA A:SER49 4.8 21.2 1.0
CG A:LYS17 4.8 29.3 1.0
CA A:GLU86 4.9 25.4 1.0
CD2 A:PHE28 5.0 22.3 1.0
CG A:TYR91 5.0 27.3 1.0

Zinc binding site 4 out of 14 in 6f06

Go back to Zinc Binding Sites List in 6f06
Zinc binding site 4 out of 14 in the Cathepsin L in Complex with (3S,14E)-8-(Azetidin-3-Yl)-19-Chloro-N-(1- Cyanocyclopropyl)-5-Oxo-12,17-Dioxa-4-Azatricyclo[16.2.2.06, 11]Docosa-1(21),6,8,10,14,18(22),19-Heptaene-3-Carboxamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cathepsin L in Complex with (3S,14E)-8-(Azetidin-3-Yl)-19-Chloro-N-(1- Cyanocyclopropyl)-5-Oxo-12,17-Dioxa-4-Azatricyclo[16.2.2.06, 11]Docosa-1(21),6,8,10,14,18(22),19-Heptaene-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn305

b:42.6
occ:1.00
 O A:HOH403 1.8 23.9 1.0
OE1 A:GLU96 2.1 37.5 1.0
OE1 A:GLU92 2.2 35.0 1.0
OE2 A:GLU96 2.2 35.6 1.0
CD A:GLU96 2.5 36.7 1.0
OE2 A:GLU92 2.6 31.7 1.0
CD A:GLU92 2.7 32.5 1.0
CG A:GLU96 4.0 34.9 1.0
CG A:GLU92 4.2 31.1 1.0
NZ A:LYS99 4.7 38.1 1.0
CB A:GLU96 4.8 33.6 1.0
CB A:GLU92 4.9 30.7 1.0
O A:HOH452 5.0 30.1 1.0

Zinc binding site 5 out of 14 in 6f06

Go back to Zinc Binding Sites List in 6f06
Zinc binding site 5 out of 14 in the Cathepsin L in Complex with (3S,14E)-8-(Azetidin-3-Yl)-19-Chloro-N-(1- Cyanocyclopropyl)-5-Oxo-12,17-Dioxa-4-Azatricyclo[16.2.2.06, 11]Docosa-1(21),6,8,10,14,18(22),19-Heptaene-3-Carboxamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Cathepsin L in Complex with (3S,14E)-8-(Azetidin-3-Yl)-19-Chloro-N-(1- Cyanocyclopropyl)-5-Oxo-12,17-Dioxa-4-Azatricyclo[16.2.2.06, 11]Docosa-1(21),6,8,10,14,18(22),19-Heptaene-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn306

b:31.5
occ:1.00
 OD2 A:ASP71 1.8 25.8 1.0
OD1 A:ASP114 1.9 28.1 1.0
CG A:ASP71 2.8 23.4 1.0
CG A:ASP114 2.9 28.3 1.0
OD1 A:ASP71 3.1 23.3 1.0
OD2 A:ASP114 3.2 28.8 1.0
O A:HOH446 3.8 33.8 1.0
CB A:SER216 4.1 27.8 1.0
CB A:ASP71 4.1 23.1 1.0
CB A:ASP114 4.1 27.8 1.0
CE2 A:PHE112 4.2 27.8 1.0
OG A:SER216 4.4 26.6 1.0
O A:HOH444 4.5 23.0 1.0
CA A:ASP114 4.6 27.1 1.0
CD2 A:PHE112 4.7 28.4 1.0

Zinc binding site 6 out of 14 in 6f06

Go back to Zinc Binding Sites List in 6f06
Zinc binding site 6 out of 14 in the Cathepsin L in Complex with (3S,14E)-8-(Azetidin-3-Yl)-19-Chloro-N-(1- Cyanocyclopropyl)-5-Oxo-12,17-Dioxa-4-Azatricyclo[16.2.2.06, 11]Docosa-1(21),6,8,10,14,18(22),19-Heptaene-3-Carboxamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Cathepsin L in Complex with (3S,14E)-8-(Azetidin-3-Yl)-19-Chloro-N-(1- Cyanocyclopropyl)-5-Oxo-12,17-Dioxa-4-Azatricyclo[16.2.2.06, 11]Docosa-1(21),6,8,10,14,18(22),19-Heptaene-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn307

b:67.9
occ:1.00
 ND1 A:HIS140 2.1 36.7 1.0
OD2 A:ASP155 2.6 49.2 1.0
OE2 A:GLU153 2.7 38.5 1.0
CD A:GLU153 2.8 37.5 1.0
CG A:HIS140 2.8 36.6 1.0
CE1 A:HIS140 3.0 36.7 1.0
CB A:HIS140 3.2 35.3 1.0
OE1 A:GLU153 3.2 40.0 1.0
CG A:GLU153 3.4 35.1 1.0
CG A:ASP155 3.5 52.8 1.0
O A:HOH443 3.8 30.2 1.0
OD1 A:ASP155 3.8 61.4 1.0
CD2 A:HIS140 3.9 34.1 1.0
NE2 A:HIS140 3.9 35.8 1.0
CA A:HIS140 4.3 35.9 1.0
CB A:ASP155 4.7 48.5 1.0
N A:ASP155 4.8 40.8 1.0
C A:ASP155 4.8 41.6 1.0
CB A:GLU153 4.9 33.0 1.0
OG A:SER142 4.9 31.7 1.0
CA A:ASP155 4.9 43.5 1.0

Zinc binding site 7 out of 14 in 6f06

Go back to Zinc Binding Sites List in 6f06
Zinc binding site 7 out of 14 in the Cathepsin L in Complex with (3S,14E)-8-(Azetidin-3-Yl)-19-Chloro-N-(1- Cyanocyclopropyl)-5-Oxo-12,17-Dioxa-4-Azatricyclo[16.2.2.06, 11]Docosa-1(21),6,8,10,14,18(22),19-Heptaene-3-Carboxamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Cathepsin L in Complex with (3S,14E)-8-(Azetidin-3-Yl)-19-Chloro-N-(1- Cyanocyclopropyl)-5-Oxo-12,17-Dioxa-4-Azatricyclo[16.2.2.06, 11]Docosa-1(21),6,8,10,14,18(22),19-Heptaene-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:28.9
occ:1.00
 O B:HOH408 2.0 35.0 1.0
ND1 B:HIS163 2.1 26.2 1.0
CL B:CL310 2.2 33.4 1.0
SG B:CYS25 2.3 25.7 1.0
CE1 B:HIS163 3.0 23.9 1.0
CB B:CYS25 3.0 24.7 1.0
N30 B:C7T301 3.1 32.8 1.0
CG B:HIS163 3.1 26.1 1.0
CB B:HIS163 3.5 25.7 1.0
CA B:HIS163 3.6 24.2 1.0
C29 B:C7T301 3.6 33.1 1.0
O B:ASP162 3.9 27.0 1.0
NE2 B:HIS163 4.1 25.2 1.0
CD2 B:HIS163 4.2 23.8 1.0
N B:GLY164 4.3 25.8 1.0
CA B:CYS25 4.3 24.3 1.0
C B:HIS163 4.4 24.6 1.0
N B:CYS25 4.5 24.7 1.0
C2 B:C7T301 4.6 34.3 1.0
N B:HIS163 4.6 24.7 1.0
NE2 B:GLN19 4.6 21.9 1.0
C B:ASP162 4.7 28.0 1.0
N16 B:C7T301 4.7 35.4 1.0
OE1 B:GLN19 4.9 22.6 1.0
CZ2 B:TRP189 4.9 27.5 1.0
NE1 B:TRP189 5.0 27.2 1.0

Zinc binding site 8 out of 14 in 6f06

Go back to Zinc Binding Sites List in 6f06
Zinc binding site 8 out of 14 in the Cathepsin L in Complex with (3S,14E)-8-(Azetidin-3-Yl)-19-Chloro-N-(1- Cyanocyclopropyl)-5-Oxo-12,17-Dioxa-4-Azatricyclo[16.2.2.06, 11]Docosa-1(21),6,8,10,14,18(22),19-Heptaene-3-Carboxamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Cathepsin L in Complex with (3S,14E)-8-(Azetidin-3-Yl)-19-Chloro-N-(1- Cyanocyclopropyl)-5-Oxo-12,17-Dioxa-4-Azatricyclo[16.2.2.06, 11]Docosa-1(21),6,8,10,14,18(22),19-Heptaene-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn303

b:42.6
occ:1.00
 OD2 B:ASP137 1.9 32.5 1.0
O B:HOH441 2.0 43.7 1.0
NE2 B:HIS140 2.1 35.4 1.0
CG B:ASP137 2.8 33.4 1.0
CE1 B:HIS140 2.8 35.2 1.0
OD1 B:ASP137 3.0 31.4 1.0
CD2 B:HIS140 3.2 33.7 1.0
ND1 B:HIS140 4.0 33.1 1.0
O B:ASP155 4.0 34.7 1.0
N B:SER157 4.1 30.5 1.0
CB B:ASP137 4.2 31.3 1.0
CG B:HIS140 4.2 34.2 1.0
CA B:CYS156 4.3 32.2 1.0
CB B:SER157 4.3 36.7 1.0
C B:CYS156 4.5 31.2 1.0
CA B:SER157 4.8 35.7 1.0
C B:ASP155 4.9 33.1 1.0
O B:ASP160 5.0 40.7 1.0
SG B:CYS156 5.0 31.3 1.0

Zinc binding site 9 out of 14 in 6f06

Go back to Zinc Binding Sites List in 6f06
Zinc binding site 9 out of 14 in the Cathepsin L in Complex with (3S,14E)-8-(Azetidin-3-Yl)-19-Chloro-N-(1- Cyanocyclopropyl)-5-Oxo-12,17-Dioxa-4-Azatricyclo[16.2.2.06, 11]Docosa-1(21),6,8,10,14,18(22),19-Heptaene-3-Carboxamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Cathepsin L in Complex with (3S,14E)-8-(Azetidin-3-Yl)-19-Chloro-N-(1- Cyanocyclopropyl)-5-Oxo-12,17-Dioxa-4-Azatricyclo[16.2.2.06, 11]Docosa-1(21),6,8,10,14,18(22),19-Heptaene-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn304

b:35.7
occ:1.00
 OE1 B:GLU9 1.9 30.1 1.0
OD2 B:ASP6 2.2 33.4 1.0
CD B:GLU9 3.0 33.1 1.0
CG B:ASP6 3.1 32.4 1.0
CB B:ASP6 3.3 33.2 1.0
CG B:GLU9 3.5 32.2 1.0
NH2 B:ARG8 3.8 27.6 1.0
OE2 B:GLU9 4.1 32.7 1.0
OD1 B:ASP6 4.2 34.0 1.0
CZ B:ARG8 4.7 27.1 1.0
NE B:ARG8 4.7 26.8 1.0
CA B:ASP6 4.9 31.1 1.0
CB B:GLU9 4.9 31.1 1.0

Zinc binding site 10 out of 14 in 6f06

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Zinc binding site 10 out of 14 in the Cathepsin L in Complex with (3S,14E)-8-(Azetidin-3-Yl)-19-Chloro-N-(1- Cyanocyclopropyl)-5-Oxo-12,17-Dioxa-4-Azatricyclo[16.2.2.06, 11]Docosa-1(21),6,8,10,14,18(22),19-Heptaene-3-Carboxamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Cathepsin L in Complex with (3S,14E)-8-(Azetidin-3-Yl)-19-Chloro-N-(1- Cyanocyclopropyl)-5-Oxo-12,17-Dioxa-4-Azatricyclo[16.2.2.06, 11]Docosa-1(21),6,8,10,14,18(22),19-Heptaene-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn305

b:33.6
occ:1.00
 OE2 B:GLU86 1.9 32.1 1.0
OE1 B:GLU50 2.0 32.7 1.0
O B:HOH419 2.0 26.9 1.0
O B:HOH434 2.1 21.5 1.0
CD B:GLU50 2.8 29.4 1.0
CD B:GLU86 2.9 34.4 1.0
OE2 B:GLU50 2.9 29.7 1.0
O B:LEU48 3.4 30.4 1.0
CG B:GLU86 3.5 32.5 1.0
OE1 B:GLU86 3.8 37.5 1.0
O B:HOH414 3.9 31.6 1.0
O B:HOH421 3.9 32.5 1.0
CB B:GLU86 4.0 34.4 1.0
CG B:GLU50 4.2 29.0 1.0
N B:GLU50 4.2 33.3 1.0
OG B:SER47 4.3 41.3 1.0
CE2 B:PHE28 4.4 22.2 1.0
CE B:LYS17 4.4 25.9 1.0
CB B:TYR91 4.4 32.4 1.0
C B:LEU48 4.5 32.2 1.0
CB B:GLU50 4.6 28.0 1.0
CG B:LYS17 4.7 24.3 1.0
CZ B:PHE28 4.9 21.9 1.0
CA B:SER49 4.9 34.6 1.0
CA B:GLU86 4.9 36.3 1.0
CD B:LYS17 5.0 25.0 1.0

Reference:

M.Giroud, U.Dietzel, L.Anselm, D.Banner, A.Kuglstatter, J.Benz, J.B.Blanc, D.Gaufreteau, H.Liu, X.Lin, A.Stich, B.Kuhn, F.Schuler, M.Kaiser, R.Brun, T.Schirmeister, C.Kisker, F.Diederich, W.Haap. Repurposing A Library of Human Cathepsin L Ligands: Identification of Macrocyclic Lactams As Potent Rhodesain and Trypanosoma Brucei Inhibitors. J. Med. Chem. V. 61 3350 2018.
ISSN: ISSN 1520-4804
PubMed: 29590750
DOI: 10.1021/ACS.JMEDCHEM.7B01869
Page generated: Mon Oct 28 20:34:38 2024

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