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Zinc in PDB 4zx8: X-Ray Crystal Structure of Pfa-M17 in Complex with Hydroxamic Acid- Based Inhibitor 9B

Enzymatic activity of X-Ray Crystal Structure of Pfa-M17 in Complex with Hydroxamic Acid- Based Inhibitor 9B

All present enzymatic activity of X-Ray Crystal Structure of Pfa-M17 in Complex with Hydroxamic Acid- Based Inhibitor 9B:
3.4.11.1;

Protein crystallography data

The structure of X-Ray Crystal Structure of Pfa-M17 in Complex with Hydroxamic Acid- Based Inhibitor 9B, PDB code: 4zx8 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) 48.95 / 2.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 174.393, 177.470, 231.292, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 24.5

Other elements in 4zx8:

The structure of X-Ray Crystal Structure of Pfa-M17 in Complex with Hydroxamic Acid- Based Inhibitor 9B also contains other interesting chemical elements:

Bromine (Br) 12 atoms

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 9B (pdb code 4zx8). 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 9B, PDB code: 4zx8:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 24 in 4zx8

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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 9B


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 9B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:22.9
occ:1.00
O4 A:4TY1001 2.0 11.1 0.8
OD2 A:ASP399 2.1 17.5 1.0
NZ A:LYS374 2.2 10.6 1.0
OE2 A:GLU461 2.3 15.8 1.0
OD2 A:ASP379 2.7 14.7 1.0
CG A:ASP399 2.9 10.1 1.0
N2 A:4TY1001 2.9 9.1 0.8
OD1 A:ASP399 3.0 10.9 1.0
CE A:LYS374 3.1 8.6 1.0
ZN A:ZN1003 3.3 19.0 1.0
CD A:GLU461 3.3 12.7 1.0
CG A:ASP379 3.5 10.9 1.0
OE1 A:GLU461 3.7 16.5 1.0
C11 A:4TY1001 3.8 12.9 0.8
O3 A:4TY1001 3.9 12.3 0.8
O1 A:CO31004 4.1 10.8 1.0
CB A:ASP379 4.1 8.6 1.0
O A:THR486 4.3 6.1 1.0
CB A:ASP399 4.4 8.8 1.0
OD1 A:ASP379 4.4 10.7 1.0
CD A:LYS374 4.5 7.8 1.0
CG1 A:ILE376 4.5 9.2 1.0
CG A:GLU461 4.6 11.4 1.0
N A:GLY462 4.7 9.4 1.0
O A:ASP459 4.7 15.5 1.0
CB A:ILE376 4.7 7.5 1.0
CA A:GLY462 4.9 10.0 1.0
CG2 A:ILE376 4.9 11.0 1.0

Zinc binding site 2 out of 24 in 4zx8

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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 9B


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 9B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1003

b:19.0
occ:1.00
O A:ASP459 2.1 15.5 1.0
OD2 A:ASP379 2.1 14.7 1.0
OD1 A:ASP459 2.1 11.0 1.0
O4 A:4TY1001 2.1 11.1 0.8
O3 A:4TY1001 2.2 12.3 0.8
OE1 A:GLU461 2.3 16.5 1.0
CG A:ASP379 2.9 10.9 1.0
N2 A:4TY1001 2.9 9.1 0.8
C11 A:4TY1001 2.9 12.9 0.8
C A:ASP459 3.0 11.1 1.0
OD1 A:ASP379 3.0 10.7 1.0
CG A:ASP459 3.1 15.6 1.0
CD A:GLU461 3.2 12.7 1.0
ZN A:ZN1002 3.3 22.9 1.0
OE2 A:GLU461 3.3 15.8 1.0
CA A:ASP459 3.4 14.4 1.0
CB A:ASP459 3.8 13.8 1.0
NZ A:LYS386 3.9 11.9 1.0
OD2 A:ASP459 4.0 22.8 1.0
N A:ALA460 4.1 7.4 1.0
CE A:LYS386 4.2 9.7 1.0
N A:GLU461 4.3 5.6 1.0
CB A:ASP379 4.3 8.6 1.0
C5 A:4TY1001 4.4 11.9 0.8
CA A:ALA460 4.6 13.7 1.0
CG A:GLU461 4.6 11.4 1.0
ND2 A:ASN432 4.6 10.7 1.0
CA A:GLY381 4.7 7.8 1.0
O1 A:CO31004 4.7 10.8 1.0
N A:ASP459 4.8 16.5 1.0
N1 A:4TY1001 4.8 15.3 0.8
OD2 A:ASP399 4.8 17.5 1.0
O A:THR458 4.8 7.9 1.0

Zinc binding site 3 out of 24 in 4zx8

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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 9B


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 9B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1002

b:23.1
occ:1.00
O4 B:4TY1001 2.1 12.3 0.8
OD2 B:ASP399 2.2 12.1 1.0
OE2 B:GLU461 2.2 13.3 1.0
NZ B:LYS374 2.4 10.0 1.0
O B:HOH1162 2.5 11.0 1.0
OD2 B:ASP379 2.6 14.4 1.0
CG B:ASP399 3.0 11.2 1.0
CE B:LYS374 3.1 11.6 1.0
OD1 B:ASP399 3.1 12.7 1.0
ZN B:ZN1003 3.1 17.9 1.0
CD B:GLU461 3.2 9.7 1.0
N2 B:4TY1001 3.2 12.2 0.8
CG B:ASP379 3.4 9.6 1.0
OE1 B:GLU461 3.6 11.9 1.0
CB B:ASP379 4.0 10.7 1.0
C11 B:4TY1001 4.1 13.2 0.8
O3 B:4TY1001 4.1 13.2 0.8
O2 B:CO31004 4.2 10.7 1.0
OD1 B:ASP379 4.2 9.5 1.0
O B:THR486 4.3 11.9 1.0
CB B:ASP399 4.4 8.6 1.0
CG1 B:ILE376 4.5 10.0 1.0
CD B:LYS374 4.5 10.1 1.0
CG B:GLU461 4.5 8.3 1.0
N B:GLY462 4.6 9.9 1.0
CB B:ILE376 4.7 15.5 1.0
O B:ASP459 4.8 14.0 1.0
CA B:GLY462 4.8 10.0 1.0
CG2 B:ILE376 4.8 14.3 1.0

Zinc binding site 4 out of 24 in 4zx8

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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 9B


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 9B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1003

b:17.9
occ:1.00
O4 B:4TY1001 2.1 12.3 0.8
O B:ASP459 2.1 14.0 1.0
OD2 B:ASP379 2.1 14.4 1.0
OE1 B:GLU461 2.2 11.9 1.0
O3 B:4TY1001 2.3 13.2 0.8
OD1 B:ASP459 2.3 10.8 1.0
N2 B:4TY1001 2.9 12.2 0.8
C11 B:4TY1001 2.9 13.2 0.8
CG B:ASP379 3.0 9.6 1.0
C B:ASP459 3.0 9.8 1.0
CD B:GLU461 3.1 9.7 1.0
OD1 B:ASP379 3.1 9.5 1.0
ZN B:ZN1002 3.1 23.1 1.0
OE2 B:GLU461 3.2 13.3 1.0
CG B:ASP459 3.3 12.3 1.0
CA B:ASP459 3.6 10.0 1.0
O B:HOH1162 3.8 11.0 1.0
NZ B:LYS386 4.0 7.0 1.0
CB B:ASP459 4.0 9.5 1.0
OD2 B:ASP459 4.1 16.9 1.0
N B:ALA460 4.1 8.4 1.0
CE B:LYS386 4.2 11.9 1.0
N B:GLU461 4.3 8.8 1.0
CB B:ASP379 4.4 10.7 1.0
C5 B:4TY1001 4.4 15.3 0.8
CG B:GLU461 4.5 8.3 1.0
CA B:ALA460 4.6 15.1 1.0
O2 B:CO31004 4.6 10.7 1.0
OD2 B:ASP399 4.8 12.1 1.0
ND2 B:ASN432 4.8 7.3 1.0
N1 B:4TY1001 4.8 15.5 0.8
CA B:GLY381 4.9 9.1 1.0
O B:THR458 4.9 10.9 1.0
N B:ASP459 4.9 8.8 1.0
C B:ALA460 4.9 16.0 1.0

Zinc binding site 5 out of 24 in 4zx8

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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 9B


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 9B within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1002

b:24.4
occ:1.00
OD2 C:ASP379 2.0 18.4 1.0
O4 C:4TY1001 2.1 12.8 0.8
O C:ASP459 2.2 10.8 1.0
OE1 C:GLU461 2.2 16.3 1.0
O3 C:4TY1001 2.3 19.5 0.8
OD1 C:ASP459 2.5 9.9 1.0
CG C:ASP379 2.9 11.2 1.0
N2 C:4TY1001 2.9 15.9 0.8
C11 C:4TY1001 2.9 14.0 0.8
ZN C:ZN1003 3.0 25.2 1.0
CD C:GLU461 3.0 12.2 1.0
OE2 C:GLU461 3.0 12.6 1.0
OD1 C:ASP379 3.1 9.9 1.0
C C:ASP459 3.1 9.2 1.0
CG C:ASP459 3.4 15.1 1.0
CA C:ASP459 3.7 7.2 1.0
NZ C:LYS386 4.0 13.1 1.0
CB C:ASP459 4.1 15.3 1.0
CE C:LYS386 4.2 12.8 1.0
N C:ALA460 4.2 10.3 1.0
OD2 C:ASP459 4.2 11.9 1.0
N C:GLU461 4.3 8.8 1.0
CB C:ASP379 4.3 9.9 1.0
C5 C:4TY1001 4.4 14.9 0.8
CG C:GLU461 4.5 11.3 1.0
CA C:ALA460 4.6 9.3 1.0
OD2 C:ASP399 4.6 16.2 1.0
O1 C:CO31004 4.7 11.0 1.0
ND2 C:ASN432 4.8 7.8 1.0
N1 C:4TY1001 4.9 21.4 0.8
NZ C:LYS374 5.0 7.3 1.0
C C:ALA460 5.0 10.4 1.0

Zinc binding site 6 out of 24 in 4zx8

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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 9B


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 9B within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1003

b:25.2
occ:1.00
O4 C:4TY1001 2.0 12.8 0.8
OE2 C:GLU461 2.2 12.6 1.0
OD2 C:ASP399 2.2 16.2 1.0
NZ C:LYS374 2.3 7.3 1.0
OD2 C:ASP379 2.7 18.4 1.0
CG C:ASP399 2.9 12.4 1.0
ZN C:ZN1002 3.0 24.4 1.0
OD1 C:ASP399 3.0 10.1 1.0
N2 C:4TY1001 3.1 15.9 0.8
CE C:LYS374 3.1 7.5 1.0
CD C:GLU461 3.2 12.2 1.0
CG C:ASP379 3.5 11.2 1.0
OE1 C:GLU461 3.6 16.3 1.0
C11 C:4TY1001 3.9 14.0 0.8
O3 C:4TY1001 3.9 19.5 0.8
CB C:ASP379 4.0 9.9 1.0
O1 C:CO31004 4.1 11.0 1.0
OD1 C:ASP379 4.3 9.9 1.0
O C:THR486 4.3 8.8 1.0
CB C:ASP399 4.4 8.8 1.0
CG C:GLU461 4.5 11.3 1.0
CD C:LYS374 4.5 14.6 1.0
N C:GLY462 4.5 8.3 1.0
CG1 C:ILE376 4.5 7.0 1.0
O C:ASP459 4.7 10.8 1.0
CA C:GLY462 4.8 7.5 1.0
CB C:ILE376 4.8 11.0 1.0
CG2 C:ILE376 4.9 9.0 1.0

Zinc binding site 7 out of 24 in 4zx8

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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 9B


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 9B within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1002

b:29.4
occ:1.00
OD2 D:ASP379 2.1 17.7 1.0
O D:ASP459 2.1 18.2 1.0
O3 D:4TY1001 2.2 15.3 0.8
O4 D:4TY1001 2.2 16.4 0.8
OE1 D:GLU461 2.3 15.3 1.0
OD1 D:ASP459 2.3 19.0 1.0
CG D:ASP379 2.9 14.0 1.0
C11 D:4TY1001 3.0 15.8 0.8
N2 D:4TY1001 3.0 13.6 0.8
OD1 D:ASP379 3.0 17.6 1.0
C D:ASP459 3.1 10.6 1.0
CD D:GLU461 3.1 12.2 1.0
ZN D:ZN1003 3.2 26.7 1.0
OE2 D:GLU461 3.2 12.4 1.0
CG D:ASP459 3.3 15.4 1.0
CA D:ASP459 3.6 9.9 1.0
NZ D:LYS386 3.9 13.5 1.0
CB D:ASP459 4.0 10.7 1.0
OD2 D:ASP459 4.1 18.3 1.0
CE D:LYS386 4.2 8.2 1.0
N D:ALA460 4.2 7.5 1.0
CB D:ASP379 4.3 10.0 1.0
N D:GLU461 4.3 9.1 1.0
C5 D:4TY1001 4.4 14.8 0.8
CG D:GLU461 4.6 9.6 1.0
ND2 D:ASN432 4.6 9.7 1.0
CA D:ALA460 4.6 9.6 1.0
O3 D:CO31004 4.6 12.4 1.0
OD2 D:ASP399 4.7 19.4 1.0
N1 D:4TY1001 4.8 15.5 0.8
CA D:GLY381 4.8 11.7 1.0
N D:ASP459 4.9 12.3 1.0

Zinc binding site 8 out of 24 in 4zx8

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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 9B


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 9B within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1003

b:26.7
occ:1.00
OD2 D:ASP399 2.0 19.4 1.0
O4 D:4TY1001 2.0 16.4 0.8
OE2 D:GLU461 2.3 12.4 1.0
NZ D:LYS374 2.4 7.3 1.0
OD2 D:ASP379 2.7 17.7 1.0
CG D:ASP399 2.8 17.3 1.0
OD1 D:ASP399 2.9 15.2 1.0
N2 D:4TY1001 3.0 13.6 0.8
CE D:LYS374 3.0 7.0 1.0
ZN D:ZN1002 3.2 29.4 1.0
CD D:GLU461 3.3 12.2 1.0
CG D:ASP379 3.4 14.0 1.0
OE1 D:GLU461 3.7 15.3 1.0
C11 D:4TY1001 3.8 15.8 0.8
O3 D:4TY1001 3.9 15.3 0.8
CB D:ASP379 4.0 10.0 1.0
CB D:ASP399 4.2 5.7 1.0
O3 D:CO31004 4.2 12.4 1.0
OD1 D:ASP379 4.3 17.6 1.0
O D:THR486 4.3 11.1 1.0
CG1 D:ILE376 4.4 9.5 1.0
CD D:LYS374 4.4 8.1 1.0
CG D:GLU461 4.6 9.6 1.0
CB D:ILE376 4.7 9.1 1.0
N D:GLY462 4.8 8.6 1.0
O D:ASP459 4.8 18.2 1.0
CG2 D:ILE376 4.9 9.7 1.0
CA D:GLY462 5.0 7.5 1.0

Zinc binding site 9 out of 24 in 4zx8

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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 9B


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 9B within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn1002

b:23.3
occ:1.00
OD2 E:ASP399 2.2 20.1 1.0
O4 E:4TY1001 2.2 11.2 0.8
NZ E:LYS374 2.3 12.3 1.0
OE2 E:GLU461 2.3 15.8 1.0
OD2 E:ASP379 2.7 16.7 1.0
CG E:ASP399 2.9 22.8 1.0
OD1 E:ASP399 2.9 19.6 1.0
N2 E:4TY1001 3.1 14.8 0.8
CE E:LYS374 3.1 9.4 1.0
ZN E:ZN1003 3.2 25.3 1.0
CD E:GLU461 3.4 16.8 1.0
CG E:ASP379 3.5 13.2 1.0
C11 E:4TY1001 3.7 15.3 0.8
O3 E:4TY1001 3.7 14.4 0.8
OE1 E:GLU461 3.8 22.6 1.0
CB E:ASP379 4.0 13.3 1.0
O E:THR486 4.2 10.3 1.0
O1 E:CO31004 4.3 11.2 1.0
CB E:ASP399 4.3 15.1 1.0
OD1 E:ASP379 4.4 10.4 1.0
CD E:LYS374 4.5 13.0 1.0
CG1 E:ILE376 4.6 8.6 1.0
N E:GLY462 4.6 12.7 1.0
CG E:GLU461 4.7 12.6 1.0
O E:ASP459 4.7 16.7 1.0
C3 E:4TY1001 4.8 12.8 0.8
CA E:GLY462 4.8 16.9 1.0
CB E:ILE376 4.9 12.3 1.0
C5 E:4TY1001 5.0 11.9 0.8

Zinc binding site 10 out of 24 in 4zx8

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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 9B


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 9B within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn1003

b:25.3
occ:1.00
O E:ASP459 2.0 16.7 1.0
O4 E:4TY1001 2.1 11.2 0.8
OD2 E:ASP379 2.1 16.7 1.0
O3 E:4TY1001 2.2 14.4 0.8
OE1 E:GLU461 2.3 22.6 1.0
OD1 E:ASP459 2.3 10.5 1.0
N2 E:4TY1001 2.8 14.8 0.8
C11 E:4TY1001 2.8 15.3 0.8
CG E:ASP379 3.0 13.2 1.0
C E:ASP459 3.0 11.8 1.0
CD E:GLU461 3.1 16.8 1.0
ZN E:ZN1002 3.2 23.3 1.0
OE2 E:GLU461 3.2 15.8 1.0
OD1 E:ASP379 3.2 10.4 1.0
CG E:ASP459 3.2 13.3 1.0
CA E:ASP459 3.5 10.9 1.0
NZ E:LYS386 3.9 14.2 1.0
CB E:ASP459 3.9 7.8 1.0
OD2 E:ASP459 4.1 9.6 1.0
N E:ALA460 4.1 10.4 1.0
N E:GLU461 4.2 10.8 1.0
CE E:LYS386 4.3 10.3 1.0
C5 E:4TY1001 4.3 11.9 0.8
CB E:ASP379 4.4 13.3 1.0
CA E:ALA460 4.5 14.1 1.0
ND2 E:ASN432 4.5 8.6 1.0
CG E:GLU461 4.5 12.6 1.0
N1 E:4TY1001 4.7 18.2 0.8
OD2 E:ASP399 4.8 20.1 1.0
CA E:GLY381 4.9 8.9 1.0
N E:ASP459 4.9 11.6 1.0
C E:ALA460 4.9 13.9 1.0
O1 E:CO31004 4.9 11.2 1.0
O E:THR458 4.9 10.9 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: Wed Dec 16 06:00:31 2020

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