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Zinc in PDB 4zyq: X-Ray Crystal Structure of Pfa-M17 in Complex with Hydroxamic Acid- Based Inhibitor 10S

Enzymatic activity of X-Ray Crystal Structure of Pfa-M17 in Complex with Hydroxamic Acid- Based Inhibitor 10S

All present enzymatic activity of X-Ray Crystal Structure of Pfa-M17 in Complex with Hydroxamic Acid- Based Inhibitor 10S:
3.4.11.1;

Protein crystallography data

The structure of X-Ray Crystal Structure of Pfa-M17 in Complex with Hydroxamic Acid- Based Inhibitor 10S, PDB code: 4zyq was solved by N.Drinkwater, S.Mcgowan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.56 / 2.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 174.436, 176.565, 230.997, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 24.4

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Zinc atom in the X-Ray Crystal Structure of Pfa-M17 in Complex with Hydroxamic Acid- Based Inhibitor 10S (pdb code 4zyq). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 24 binding sites of Zinc where determined in the X-Ray Crystal Structure of Pfa-M17 in Complex with Hydroxamic Acid- Based Inhibitor 10S, PDB code: 4zyq:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 24 in 4zyq

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Zinc binding site 1 out of 24 in the X-Ray Crystal Structure of Pfa-M17 in Complex with Hydroxamic Acid- Based Inhibitor 10S


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of X-Ray Crystal Structure of Pfa-M17 in Complex with Hydroxamic Acid- Based Inhibitor 10S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:17.0
occ:1.00
 OAH A:4U61001 2.0 16.4 1.0
OE2 A:GLU461 2.1 19.6 1.0
NZ A:LYS374 2.2 11.2 1.0
OD2 A:ASP399 2.2 19.8 1.0
OD2 A:ASP379 2.7 25.3 1.0
CG A:ASP399 2.9 15.9 1.0
NAR A:4U61001 2.9 17.5 1.0
OD1 A:ASP399 3.0 18.1 1.0
CE A:LYS374 3.0 12.0 1.0
CD A:GLU461 3.1 17.1 1.0
ZN A:ZN1003 3.3 10.8 1.0
OE1 A:GLU461 3.5 14.9 1.0
CG A:ASP379 3.5 17.8 1.0
C A:4U61001 3.7 20.1 1.0
O A:4U61001 3.9 15.1 1.0
CB A:ASP379 4.0 10.6 1.0
O2 A:CO31004 4.2 16.8 1.0
O A:THR486 4.3 13.0 1.0
OD1 A:ASP379 4.3 17.6 1.0
CD A:LYS374 4.4 13.1 1.0
CB A:ASP399 4.4 22.7 1.0
CG A:GLU461 4.5 15.1 1.0
CG1 A:ILE376 4.5 17.8 1.0
N A:GLY462 4.6 11.8 1.0
O A:ASP459 4.7 19.1 1.0
CB A:ILE376 4.7 13.8 1.0
CA A:GLY462 4.8 10.4 1.0
CG2 A:ILE376 4.9 14.5 1.0

Zinc binding site 2 out of 24 in 4zyq

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Zinc binding site 2 out of 24 in the X-Ray Crystal Structure of Pfa-M17 in Complex with Hydroxamic Acid- Based Inhibitor 10S


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of X-Ray Crystal Structure of Pfa-M17 in Complex with Hydroxamic Acid- Based Inhibitor 10S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1003

b:10.8
occ:1.00
 O A:ASP459 2.1 19.1 1.0
OAH A:4U61001 2.1 16.4 1.0
OD2 A:ASP379 2.1 25.3 1.0
O A:4U61001 2.2 15.1 1.0
OD1 A:ASP459 2.2 13.7 1.0
OE1 A:GLU461 2.2 14.9 1.0
C A:4U61001 2.8 20.1 1.0
NAR A:4U61001 2.9 17.5 1.0
CG A:ASP379 2.9 17.8 1.0
C A:ASP459 3.0 12.2 1.0
OD1 A:ASP379 3.1 17.6 1.0
CG A:ASP459 3.1 17.7 1.0
CD A:GLU461 3.1 17.1 1.0
ZN A:ZN1002 3.3 17.0 1.0
OE2 A:GLU461 3.4 19.6 1.0
CA A:ASP459 3.5 13.3 1.0
CB A:ASP459 3.9 13.4 1.0
OD2 A:ASP459 3.9 21.9 1.0
NZ A:LYS386 4.0 19.0 1.0
CE A:LYS386 4.2 17.1 1.0
N A:ALA460 4.2 12.0 1.0
N A:GLU461 4.3 9.1 1.0
CA A:4U61001 4.3 23.3 1.0
CB A:ASP379 4.4 10.6 1.0
ND2 A:ASN432 4.5 14.3 1.0
CG A:GLU461 4.5 15.1 1.0
CA A:ALA460 4.6 14.0 1.0
N A:4U61001 4.7 16.1 1.0
CA A:GLY381 4.7 17.1 1.0
OD2 A:ASP399 4.8 19.8 1.0
N A:ASP459 4.8 15.7 1.0
O A:THR458 4.9 13.4 1.0
CB A:GLU461 5.0 15.1 1.0
C A:ALA460 5.0 10.9 1.0

Zinc binding site 3 out of 24 in 4zyq

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Zinc binding site 3 out of 24 in the X-Ray Crystal Structure of Pfa-M17 in Complex with Hydroxamic Acid- Based Inhibitor 10S


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of X-Ray Crystal Structure of Pfa-M17 in Complex with Hydroxamic Acid- Based Inhibitor 10S within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1002

b:15.1
occ:1.00
 OAH B:4U61001 2.0 21.8 1.0
OD2 B:ASP399 2.0 21.1 1.0
NZ B:LYS374 2.2 17.7 1.0
OE2 B:GLU461 2.3 17.9 1.0
OD2 B:ASP379 2.6 18.1 1.0
CG B:ASP399 2.8 17.0 1.0
OD1 B:ASP399 2.9 19.8 1.0
NAR B:4U61001 3.0 19.4 1.0
CE B:LYS374 3.0 13.8 1.0
ZN B:ZN1003 3.1 16.8 1.0
CD B:GLU461 3.3 17.8 1.0
CG B:ASP379 3.4 15.3 1.0
OE1 B:GLU461 3.6 13.6 1.0
C B:4U61001 3.7 21.7 1.0
O B:4U61001 3.7 20.0 1.0
CB B:ASP379 3.9 14.0 1.0
O1 B:CO31004 4.0 16.0 1.0
O B:THR486 4.1 15.8 1.0
CB B:ASP399 4.2 12.9 1.0
OD1 B:ASP379 4.3 17.6 1.0
CD B:LYS374 4.4 13.0 1.0
CG B:GLU461 4.6 16.1 1.0
CG1 B:ILE376 4.7 15.2 1.0
O B:ASP459 4.7 17.3 1.0
N B:GLY462 4.8 13.9 1.0
CB B:ILE376 4.8 20.3 1.0
CA B:4U61001 5.0 26.1 1.0
OG1 B:THR486 5.0 20.8 1.0

Zinc binding site 4 out of 24 in 4zyq

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Zinc binding site 4 out of 24 in the X-Ray Crystal Structure of Pfa-M17 in Complex with Hydroxamic Acid- Based Inhibitor 10S


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of X-Ray Crystal Structure of Pfa-M17 in Complex with Hydroxamic Acid- Based Inhibitor 10S within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1003

b:16.8
occ:1.00
 OD2 B:ASP379 2.0 18.1 1.0
O B:ASP459 2.1 17.3 1.0
OD1 B:ASP459 2.1 19.5 1.0
OE1 B:GLU461 2.1 13.6 1.0
O B:4U61001 2.2 20.0 1.0
OAH B:4U61001 2.3 21.8 1.0
CG B:ASP379 2.9 15.3 1.0
C B:4U61001 2.9 21.7 1.0
NAR B:4U61001 3.0 19.4 1.0
C B:ASP459 3.0 14.2 1.0
OD1 B:ASP379 3.0 17.6 1.0
CD B:GLU461 3.1 17.8 1.0
CG B:ASP459 3.1 17.2 1.0
ZN B:ZN1002 3.1 15.1 1.0
OE2 B:GLU461 3.3 17.9 1.0
CA B:ASP459 3.5 11.7 1.0
CB B:ASP459 3.8 10.8 1.0
OD2 B:ASP459 3.9 20.6 1.0
NZ B:LYS386 4.0 15.4 1.0
N B:ALA460 4.2 14.0 1.0
CE B:LYS386 4.2 14.4 1.0
N B:GLU461 4.3 15.1 1.0
CB B:ASP379 4.3 14.0 1.0
CA B:4U61001 4.3 26.1 1.0
CG B:GLU461 4.5 16.1 1.0
CA B:ALA460 4.6 17.7 1.0
ND2 B:ASN432 4.7 15.1 1.0
OD2 B:ASP399 4.7 21.1 1.0
N B:4U61001 4.7 25.3 1.0
O1 B:CO31004 4.7 16.0 1.0
CA B:GLY381 4.8 18.2 1.0
N B:ASP459 4.8 14.3 1.0
CB B:GLU461 4.9 11.4 1.0
O B:THR458 4.9 14.2 1.0
NZ B:LYS374 4.9 17.7 1.0
C B:ALA460 5.0 16.6 1.0

Zinc binding site 5 out of 24 in 4zyq

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Zinc binding site 5 out of 24 in the X-Ray Crystal Structure of Pfa-M17 in Complex with Hydroxamic Acid- Based Inhibitor 10S


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of X-Ray Crystal Structure of Pfa-M17 in Complex with Hydroxamic Acid- Based Inhibitor 10S within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1002

b:14.7
occ:1.00
 OAH C:4U61001 1.9 14.9 1.0
OD2 C:ASP399 2.1 15.2 1.0
OE2 C:GLU461 2.2 14.2 1.0
NZ C:LYS374 2.2 14.1 1.0
OD2 C:ASP379 2.8 21.7 1.0
CG C:ASP399 2.8 12.2 1.0
OD1 C:ASP399 2.9 15.8 1.0
NAR C:4U61001 3.0 14.2 1.0
CE C:LYS374 3.0 14.1 1.0
ZN C:ZN1003 3.1 11.9 1.0
CD C:GLU461 3.2 14.4 1.0
O C:4U61001 3.5 23.4 1.0
CG C:ASP379 3.5 12.2 1.0
C C:4U61001 3.6 22.8 1.0
OE1 C:GLU461 3.6 16.8 1.0
CB C:ASP379 4.0 10.6 1.0
O3 C:CO31004 4.1 14.8 1.0
O C:THR486 4.3 18.0 1.0
CB C:ASP399 4.3 12.5 1.0
OD1 C:ASP379 4.3 10.7 1.0
CD C:LYS374 4.4 16.1 1.0
CG C:GLU461 4.5 11.8 1.0
CG1 C:ILE376 4.5 15.6 1.0
N C:GLY462 4.6 9.9 1.0
O C:ASP459 4.6 13.7 1.0
CB C:ILE376 4.8 16.4 1.0
CA C:GLY462 4.9 11.3 1.0
CG2 C:ILE376 4.9 9.4 1.0
CA C:4U61001 4.9 23.8 1.0

Zinc binding site 6 out of 24 in 4zyq

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Zinc binding site 6 out of 24 in the X-Ray Crystal Structure of Pfa-M17 in Complex with Hydroxamic Acid- Based Inhibitor 10S


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of X-Ray Crystal Structure of Pfa-M17 in Complex with Hydroxamic Acid- Based Inhibitor 10S within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1003

b:11.9
occ:1.00
 OD2 C:ASP379 2.0 21.7 1.0
O C:ASP459 2.1 13.7 1.0
OD1 C:ASP459 2.1 21.9 1.0
O C:4U61001 2.2 23.4 1.0
OE1 C:GLU461 2.3 16.8 1.0
OAH C:4U61001 2.3 14.9 1.0
CG C:ASP379 2.8 12.2 1.0
C C:4U61001 2.8 22.8 1.0
NAR C:4U61001 3.0 14.2 1.0
OD1 C:ASP379 3.0 10.7 1.0
CD C:GLU461 3.1 14.4 1.0
C C:ASP459 3.1 13.8 1.0
CG C:ASP459 3.1 21.8 1.0
ZN C:ZN1002 3.1 14.7 1.0
OE2 C:GLU461 3.2 14.2 1.0
CA C:ASP459 3.6 8.3 1.0
CB C:ASP459 3.9 14.2 1.0
OD2 C:ASP459 3.9 17.0 1.0
NZ C:LYS386 3.9 14.6 1.0
CE C:LYS386 4.2 16.6 1.0
CB C:ASP379 4.3 10.6 1.0
N C:ALA460 4.3 15.1 1.0
CA C:4U61001 4.3 23.8 1.0
N C:GLU461 4.3 14.4 1.0
CG C:GLU461 4.5 11.8 1.0
N C:4U61001 4.6 25.6 1.0
OD2 C:ASP399 4.6 15.2 1.0
ND2 C:ASN432 4.6 7.9 1.0
CA C:ALA460 4.7 12.6 1.0
CA C:GLY381 4.8 11.9 1.0
N C:ASP459 4.9 9.3 1.0
O3 C:CO31004 4.9 14.8 1.0

Zinc binding site 7 out of 24 in 4zyq

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Zinc binding site 7 out of 24 in the X-Ray Crystal Structure of Pfa-M17 in Complex with Hydroxamic Acid- Based Inhibitor 10S


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of X-Ray Crystal Structure of Pfa-M17 in Complex with Hydroxamic Acid- Based Inhibitor 10S within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1002

b:16.7
occ:1.00
 OAH D:4U61001 1.9 20.9 1.0
OD2 D:ASP399 2.1 24.0 1.0
OE2 D:GLU461 2.1 20.5 1.0
NZ D:LYS374 2.2 19.3 1.0
OD2 D:ASP379 2.7 22.1 1.0
CG D:ASP399 2.9 22.1 1.0
NAR D:4U61001 2.9 22.9 1.0
OD1 D:ASP399 3.0 25.9 1.0
CE D:LYS374 3.0 15.0 1.0
CD D:GLU461 3.1 19.1 1.0
ZN D:ZN1003 3.1 13.8 1.0
CG D:ASP379 3.5 20.7 1.0
OE1 D:GLU461 3.5 17.9 1.0
C D:4U61001 3.6 23.8 1.0
O D:4U61001 3.7 17.0 1.0
CB D:ASP379 4.0 14.2 1.0
O1 D:CO31004 4.1 16.5 1.0
OD1 D:ASP379 4.3 24.1 1.0
CB D:ASP399 4.3 14.2 1.0
O D:THR486 4.3 22.5 1.0
CG D:GLU461 4.4 18.8 1.0
CD D:LYS374 4.4 16.5 1.0
O D:ASP459 4.5 18.8 1.0
CG1 D:ILE376 4.6 12.2 1.0
N D:GLY462 4.6 16.0 1.0
CB D:ILE376 4.8 11.7 1.0
CA D:GLY462 4.9 9.7 1.0
CA D:4U61001 4.9 19.9 1.0
CG2 D:ILE376 5.0 15.7 1.0

Zinc binding site 8 out of 24 in 4zyq

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Zinc binding site 8 out of 24 in the X-Ray Crystal Structure of Pfa-M17 in Complex with Hydroxamic Acid- Based Inhibitor 10S


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of X-Ray Crystal Structure of Pfa-M17 in Complex with Hydroxamic Acid- Based Inhibitor 10S within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1003

b:13.8
occ:1.00
 OD2 D:ASP379 2.0 22.1 1.0
O D:ASP459 2.1 18.8 1.0
O D:4U61001 2.2 17.0 1.0
OD1 D:ASP459 2.2 23.1 1.0
OE1 D:GLU461 2.2 17.9 1.0
OAH D:4U61001 2.3 20.9 1.0
C D:4U61001 2.8 23.8 1.0
CG D:ASP379 2.9 20.7 1.0
NAR D:4U61001 3.0 22.9 1.0
C D:ASP459 3.0 15.1 1.0
OD1 D:ASP379 3.0 24.1 1.0
CD D:GLU461 3.1 19.1 1.0
ZN D:ZN1002 3.1 16.7 1.0
CG D:ASP459 3.1 21.8 1.0
OE2 D:GLU461 3.3 20.5 1.0
CA D:ASP459 3.4 12.1 1.0
CB D:ASP459 3.9 18.2 1.0
NZ D:LYS386 4.0 21.2 1.0
OD2 D:ASP459 4.0 22.7 1.0
N D:ALA460 4.2 11.3 1.0
CE D:LYS386 4.2 16.4 1.0
N D:GLU461 4.3 12.4 1.0
CB D:ASP379 4.3 14.2 1.0
CA D:4U61001 4.3 19.9 1.0
ND2 D:ASN432 4.5 26.6 1.0
CG D:GLU461 4.5 18.8 1.0
OD2 D:ASP399 4.6 24.0 1.0
CA D:ALA460 4.6 13.3 1.0
N D:4U61001 4.6 18.4 1.0
N D:ASP459 4.8 15.8 1.0
CA D:GLY381 4.8 17.8 1.0
O D:THR458 4.8 18.3 1.0
CB D:GLU461 5.0 17.0 1.0
NZ D:LYS374 5.0 19.3 1.0

Zinc binding site 9 out of 24 in 4zyq

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Zinc binding site 9 out of 24 in the X-Ray Crystal Structure of Pfa-M17 in Complex with Hydroxamic Acid- Based Inhibitor 10S


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of X-Ray Crystal Structure of Pfa-M17 in Complex with Hydroxamic Acid- Based Inhibitor 10S within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn1002

b:14.4
occ:1.00
 OAH E:4U61001 2.0 23.5 1.0
OD2 E:ASP399 2.1 20.2 1.0
NZ E:LYS374 2.2 20.4 1.0
OE2 E:GLU461 2.3 16.6 1.0
OD2 E:ASP379 2.8 18.8 1.0
CG E:ASP399 2.9 16.8 1.0
NAR E:4U61001 2.9 20.1 1.0
OD1 E:ASP399 3.0 21.7 1.0
CE E:LYS374 3.0 18.5 1.0
ZN E:ZN1003 3.2 19.9 1.0
CD E:GLU461 3.3 18.2 1.0
CG E:ASP379 3.6 18.2 1.0
C E:4U61001 3.6 19.9 1.0
OE1 E:GLU461 3.6 19.4 1.0
O E:4U61001 3.7 16.6 1.0
O3 E:CO31004 3.9 20.0 1.0
CB E:ASP379 4.1 13.9 1.0
O E:THR486 4.1 13.4 1.0
CB E:ASP399 4.3 14.3 1.0
CD E:LYS374 4.4 13.8 1.0
OD1 E:ASP379 4.4 15.6 1.0
CG E:GLU461 4.6 14.5 1.0
O E:ASP459 4.6 15.0 1.0
N E:GLY462 4.7 17.1 1.0
CG1 E:ILE376 4.7 11.7 1.0
CA E:GLY462 4.9 18.0 1.0
CB E:ILE376 4.9 15.6 1.0
CA E:4U61001 4.9 18.9 1.0

Zinc binding site 10 out of 24 in 4zyq

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Zinc binding site 10 out of 24 in the X-Ray Crystal Structure of Pfa-M17 in Complex with Hydroxamic Acid- Based Inhibitor 10S


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of X-Ray Crystal Structure of Pfa-M17 in Complex with Hydroxamic Acid- Based Inhibitor 10S within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn1003

b:19.9
occ:1.00
 O E:ASP459 2.0 15.0 1.0
OD2 E:ASP379 2.1 18.8 1.0
OAH E:4U61001 2.1 23.5 1.0
OE1 E:GLU461 2.2 19.4 1.0
OD1 E:ASP459 2.2 17.9 1.0
O E:4U61001 2.3 16.6 1.0
NAR E:4U61001 2.9 20.1 1.0
C E:4U61001 2.9 19.9 1.0
CG E:ASP379 2.9 18.2 1.0
C E:ASP459 3.0 14.9 1.0
CD E:GLU461 3.1 18.2 1.0
OD1 E:ASP379 3.1 15.6 1.0
CG E:ASP459 3.2 16.4 1.0
ZN E:ZN1002 3.2 14.4 1.0
OE2 E:GLU461 3.3 16.6 1.0
CA E:ASP459 3.4 13.7 1.0
CB E:ASP459 3.9 13.7 1.0
NZ E:LYS386 3.9 17.9 1.0
OD2 E:ASP459 4.1 19.9 1.0
N E:ALA460 4.1 10.4 1.0
CE E:LYS386 4.1 15.9 1.0
N E:GLU461 4.2 18.4 1.0
CB E:ASP379 4.3 13.9 1.0
CA E:4U61001 4.3 18.9 1.0
ND2 E:ASN432 4.4 10.6 1.0
CG E:GLU461 4.5 14.5 1.0
CA E:ALA460 4.6 15.8 1.0
N E:4U61001 4.7 19.6 1.0
O3 E:CO31004 4.7 20.0 1.0
CA E:GLY381 4.7 12.0 1.0
OD2 E:ASP399 4.7 20.2 1.0
N E:ASP459 4.8 13.3 1.0
O E:THR458 4.8 15.7 1.0
CB E:GLU461 4.9 14.8 1.0
C E:ALA460 5.0 17.2 1.0

Reference:

N.Drinkwater, N.B.Vinh, S.N.Mistry, R.S.Bamert, C.Ruggeri, J.P.Holleran, S.Loganathan, A.Paiardini, S.A.Charman, A.K.Powell, V.M.Avery, S.Mcgowan, P.J.Scammells. Potent Dual Inhibitors of Plasmodium Falciparum M1 and M17 Aminopeptidases Through Optimization of S1 Pocket Interactions. Eur.J.Med.Chem. V. 110 43 2016.
ISSN: ISSN 0223-5234
PubMed: 26807544
DOI: 10.1016/J.EJMECH.2016.01.015
Page generated: Sun Oct 27 12:13:27 2024

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