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Magnesium in PDB 4dxj: Crystal Structure of Trypanosome Cruzi Farnesyl Diphosphate Synthase in Complex with [2-(N-Propylamino)Ethane-1,1-Diyl]Bisphosphonic Acid and MG2+

Enzymatic activity of Crystal Structure of Trypanosome Cruzi Farnesyl Diphosphate Synthase in Complex with [2-(N-Propylamino)Ethane-1,1-Diyl]Bisphosphonic Acid and MG2+

All present enzymatic activity of Crystal Structure of Trypanosome Cruzi Farnesyl Diphosphate Synthase in Complex with [2-(N-Propylamino)Ethane-1,1-Diyl]Bisphosphonic Acid and MG2+:
2.5.1.10;

Protein crystallography data

The structure of Crystal Structure of Trypanosome Cruzi Farnesyl Diphosphate Synthase in Complex with [2-(N-Propylamino)Ethane-1,1-Diyl]Bisphosphonic Acid and MG2+, PDB code: 4dxj was solved by S.Aripirala, L.M.Amzel, S.B.Gabelli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.72 / 2.35
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 103.220, 103.220, 386.658, 90.00, 90.00, 120.00
R / Rfree (%) 22 / 28.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Trypanosome Cruzi Farnesyl Diphosphate Synthase in Complex with [2-(N-Propylamino)Ethane-1,1-Diyl]Bisphosphonic Acid and MG2+ (pdb code 4dxj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Crystal Structure of Trypanosome Cruzi Farnesyl Diphosphate Synthase in Complex with [2-(N-Propylamino)Ethane-1,1-Diyl]Bisphosphonic Acid and MG2+, PDB code: 4dxj:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 4dxj

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Magnesium binding site 1 out of 9 in the Crystal Structure of Trypanosome Cruzi Farnesyl Diphosphate Synthase in Complex with [2-(N-Propylamino)Ethane-1,1-Diyl]Bisphosphonic Acid and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Trypanosome Cruzi Farnesyl Diphosphate Synthase in Complex with [2-(N-Propylamino)Ethane-1,1-Diyl]Bisphosphonic Acid and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:35.4
occ:1.00
 O6 A:0M9404 1.9 33.1 1.0
OD1 A:ASP98 2.1 33.4 1.0
O A:HOH508 2.1 23.1 1.0
O A:HOH507 2.1 25.7 1.0
OD2 A:ASP102 2.2 32.0 1.0
O A:HOH506 2.3 17.8 1.0
CG A:ASP98 3.0 32.0 1.0
P2 A:0M9404 3.1 33.2 1.0
MG A:MG402 3.1 35.3 1.0
CG A:ASP102 3.2 34.0 1.0
OD2 A:ASP98 3.2 34.4 1.0
O4 A:0M9404 3.3 32.7 1.0
OD1 A:ASP102 3.4 33.5 1.0
OD2 A:ASP170 3.9 30.0 1.0
C9 A:0M9404 3.9 34.9 1.0
O A:HOH504 4.0 30.4 1.0
NE2 A:GLN167 4.2 26.8 1.0
N1 A:0M9404 4.2 34.3 1.0
CG A:ASP170 4.3 30.6 1.0
O5 A:0M9404 4.3 35.0 1.0
CB A:ASP98 4.4 30.1 1.0
OE1 A:GLN167 4.4 31.1 1.0
OD1 A:ASP170 4.4 30.3 1.0
NZ A:LYS273 4.4 32.3 1.0
CB A:ASP102 4.6 34.0 1.0
C8 A:0M9404 4.7 35.4 1.0
CD A:GLN167 4.7 30.1 1.0
O A:ASP98 4.7 31.1 1.0
O2 A:0M9404 4.9 34.6 1.0
NZ A:LYS207 4.9 28.9 1.0

Magnesium binding site 2 out of 9 in 4dxj

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Magnesium binding site 2 out of 9 in the Crystal Structure of Trypanosome Cruzi Farnesyl Diphosphate Synthase in Complex with [2-(N-Propylamino)Ethane-1,1-Diyl]Bisphosphonic Acid and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Trypanosome Cruzi Farnesyl Diphosphate Synthase in Complex with [2-(N-Propylamino)Ethane-1,1-Diyl]Bisphosphonic Acid and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:35.3
occ:1.00
 O A:HOH504 2.1 30.4 1.0
OD2 A:ASP98 2.1 34.4 1.0
O2 A:0M9404 2.2 34.6 1.0
O6 A:0M9404 2.2 33.1 1.0
O A:HOH505 2.4 28.9 1.0
OD2 A:ASP102 2.4 32.0 1.0
C9 A:0M9404 3.0 34.9 1.0
MG A:MG401 3.1 35.4 1.0
P1 A:0M9404 3.1 35.2 1.0
CG A:ASP98 3.1 32.0 1.0
P2 A:0M9404 3.2 33.2 1.0
CG A:ASP102 3.5 34.0 1.0
OD1 A:ASP98 3.5 33.4 1.0
O3 A:0M9404 3.8 36.3 1.0
O A:HOH510 3.9 17.2 1.0
CB A:ASP102 3.9 34.0 1.0
O5 A:0M9404 4.0 35.0 1.0
O A:HOH503 4.1 19.9 1.0
NH2 A:ARG107 4.2 36.1 1.0
O A:HOH508 4.2 23.1 1.0
O A:ASP98 4.3 31.1 1.0
C8 A:0M9404 4.4 35.4 1.0
O1 A:0M9404 4.4 36.3 1.0
O4 A:0M9404 4.4 32.7 1.0
CB A:ASP98 4.5 30.1 1.0
OD1 A:ASP99 4.5 31.1 1.0
OD1 A:ASP102 4.5 33.5 1.0
OG A:SER104 4.6 36.5 1.0
N1 A:0M9404 4.6 34.3 1.0
C A:ASP98 4.7 30.7 1.0
MG A:MG403 4.8 34.9 1.0
O A:HOH511 4.8 28.2 1.0
O A:HOH507 4.9 25.7 1.0
O A:HOH506 5.0 17.8 1.0

Magnesium binding site 3 out of 9 in 4dxj

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Magnesium binding site 3 out of 9 in the Crystal Structure of Trypanosome Cruzi Farnesyl Diphosphate Synthase in Complex with [2-(N-Propylamino)Ethane-1,1-Diyl]Bisphosphonic Acid and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Trypanosome Cruzi Farnesyl Diphosphate Synthase in Complex with [2-(N-Propylamino)Ethane-1,1-Diyl]Bisphosphonic Acid and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:34.9
occ:1.00
 O3 A:0M9404 1.8 36.3 1.0
O A:HOH501 2.0 21.9 1.0
O5 A:0M9404 2.0 35.0 1.0
O A:HOH502 2.1 36.1 1.0
O A:HOH503 2.1 19.9 1.0
OD2 A:ASP250 2.1 33.4 1.0
CG A:ASP250 3.1 35.1 1.0
P1 A:0M9404 3.3 35.2 1.0
P2 A:0M9404 3.4 33.2 1.0
OD1 A:ASP250 3.6 36.9 1.0
C9 A:0M9404 3.9 34.9 1.0
O A:HOH504 4.0 30.4 1.0
OD1 A:ASP254 4.0 40.0 1.0
OD2 A:ASP268 4.1 39.6 1.0
O2 A:0M9404 4.1 34.6 1.0
O6 A:0M9404 4.2 33.1 1.0
NZ A:LYS264 4.2 40.7 1.0
O A:ASP250 4.2 35.5 1.0
O1 A:0M9404 4.2 36.3 1.0
NE2 A:GLN247 4.3 30.8 1.0
OD1 A:ASP268 4.4 37.8 1.0
CB A:ASP250 4.4 34.6 1.0
C A:ASP250 4.5 35.6 1.0
OD1 A:ASP251 4.5 35.9 1.0
O4 A:0M9404 4.5 32.7 1.0
CB A:ASP254 4.6 39.1 1.0
CG A:ASP254 4.6 39.0 1.0
CG A:ASP268 4.6 39.0 1.0
CE A:LYS264 4.7 41.1 1.0
C8 A:0M9404 4.8 35.4 1.0
MG A:MG402 4.8 35.3 1.0
O A:HOH510 4.9 17.2 1.0
N A:ASP251 4.9 35.4 1.0

Magnesium binding site 4 out of 9 in 4dxj

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Magnesium binding site 4 out of 9 in the Crystal Structure of Trypanosome Cruzi Farnesyl Diphosphate Synthase in Complex with [2-(N-Propylamino)Ethane-1,1-Diyl]Bisphosphonic Acid and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Trypanosome Cruzi Farnesyl Diphosphate Synthase in Complex with [2-(N-Propylamino)Ethane-1,1-Diyl]Bisphosphonic Acid and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:33.6
occ:1.00
 O5 B:0M9404 1.9 34.0 1.0
O B:HOH557 1.9 19.6 1.0
OD1 B:ASP98 2.0 29.7 1.0
O B:HOH556 2.1 15.9 1.0
O B:HOH558 2.1 27.3 1.0
OD2 B:ASP102 2.4 29.4 1.0
CG B:ASP98 3.1 29.6 1.0
P2 B:0M9404 3.1 33.1 1.0
CG B:ASP102 3.2 31.8 1.0
MG B:MG402 3.2 30.9 1.0
O4 B:0M9404 3.2 34.2 1.0
OD1 B:ASP102 3.3 29.8 1.0
OD2 B:ASP98 3.5 30.6 1.0
OD2 B:ASP170 3.5 32.0 1.0
C9 B:0M9404 4.0 34.7 1.0
O B:HOH554 4.1 31.4 1.0
NE2 B:GLN167 4.1 29.1 1.0
NZ B:LYS273 4.2 29.6 1.0
OE1 B:GLN167 4.2 29.5 1.0
CG B:ASP170 4.2 33.0 1.0
O B:HOH501 4.2 17.6 1.0
O6 B:0M9404 4.3 32.2 1.0
CB B:ASP98 4.4 28.7 1.0
OD1 B:ASP170 4.5 33.0 1.0
N1 B:0M9404 4.5 32.4 1.0
CD B:GLN167 4.6 30.3 1.0
CB B:ASP102 4.6 31.8 1.0
O B:ASP98 4.8 29.3 1.0
C8 B:0M9404 4.9 32.9 1.0
O B:HOH555 4.9 18.6 1.0
O3 B:0M9404 5.0 34.7 1.0
NZ B:LYS207 5.0 28.3 1.0

Magnesium binding site 5 out of 9 in 4dxj

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Magnesium binding site 5 out of 9 in the Crystal Structure of Trypanosome Cruzi Farnesyl Diphosphate Synthase in Complex with [2-(N-Propylamino)Ethane-1,1-Diyl]Bisphosphonic Acid and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Trypanosome Cruzi Farnesyl Diphosphate Synthase in Complex with [2-(N-Propylamino)Ethane-1,1-Diyl]Bisphosphonic Acid and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:30.9
occ:1.00
 O B:HOH554 1.8 31.4 1.0
O3 B:0M9404 2.0 34.7 1.0
O5 B:0M9404 2.1 34.0 1.0
OD2 B:ASP102 2.2 29.4 1.0
O B:HOH555 2.2 18.6 1.0
OD2 B:ASP98 2.2 30.6 1.0
C9 B:0M9404 2.9 34.7 1.0
P1 B:0M9404 3.0 33.2 1.0
P2 B:0M9404 3.0 33.1 1.0
CG B:ASP98 3.1 29.6 1.0
MG B:MG401 3.2 33.6 1.0
CG B:ASP102 3.3 31.8 1.0
OD1 B:ASP98 3.4 29.7 1.0
O2 B:0M9404 3.6 34.7 1.0
O6 B:0M9404 3.7 32.2 1.0
O B:HOH559 3.9 14.5 1.0
CB B:ASP102 3.9 31.8 1.0
NH2 B:ARG107 4.1 28.4 1.0
O B:HOH553 4.2 21.8 1.0
O B:HOH558 4.2 27.3 1.0
O1 B:0M9404 4.3 33.5 1.0
O4 B:0M9404 4.3 34.2 1.0
C8 B:0M9404 4.3 32.9 1.0
OD1 B:ASP102 4.4 29.8 1.0
O B:ASP98 4.5 29.3 1.0
CB B:ASP98 4.5 28.7 1.0
OD1 B:ASP99 4.6 27.4 1.0
OG B:SER104 4.6 33.0 1.0
N1 B:0M9404 4.7 32.4 1.0
O B:HOH560 4.8 24.4 1.0
C B:ASP98 4.8 29.1 1.0
MG B:MG403 4.8 28.6 1.0
O B:HOH501 4.8 17.6 1.0
O B:HOH557 4.8 19.6 1.0
O B:HOH556 4.9 15.9 1.0

Magnesium binding site 6 out of 9 in 4dxj

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Magnesium binding site 6 out of 9 in the Crystal Structure of Trypanosome Cruzi Farnesyl Diphosphate Synthase in Complex with [2-(N-Propylamino)Ethane-1,1-Diyl]Bisphosphonic Acid and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Trypanosome Cruzi Farnesyl Diphosphate Synthase in Complex with [2-(N-Propylamino)Ethane-1,1-Diyl]Bisphosphonic Acid and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:28.6
occ:1.00
 O2 B:0M9404 1.9 34.7 1.0
O B:HOH552 2.0 25.3 1.0
O B:HOH551 2.0 21.7 1.0
OD2 B:ASP250 2.1 31.8 1.0
O6 B:0M9404 2.1 32.2 1.0
O B:HOH553 2.1 21.8 1.0
CG B:ASP250 3.1 32.6 1.0
P1 B:0M9404 3.4 33.2 1.0
P2 B:0M9404 3.5 33.1 1.0
OD1 B:ASP250 3.5 32.6 1.0
OD1 B:ASP254 3.8 38.9 1.0
C9 B:0M9404 4.0 34.7 1.0
O B:HOH501 4.0 17.6 1.0
O B:ASP250 4.2 33.6 1.0
NE2 B:GLN247 4.2 25.6 1.0
NZ B:LYS264 4.3 36.0 1.0
O3 B:0M9404 4.3 34.7 1.0
CB B:ASP250 4.3 32.1 1.0
O1 B:0M9404 4.3 33.5 1.0
O5 B:0M9404 4.4 34.0 1.0
OD2 B:ASP268 4.4 32.5 1.0
OD1 B:ASP268 4.4 32.0 1.0
O B:HOH554 4.4 31.4 1.0
C B:ASP250 4.5 32.8 1.0
CG B:ASP254 4.5 37.1 1.0
OD1 B:ASP251 4.5 30.1 1.0
O4 B:0M9404 4.5 34.2 1.0
CB B:ASP254 4.7 36.4 1.0
C8 B:0M9404 4.7 32.9 1.0
O B:HOH559 4.7 14.5 1.0
CG B:ASP268 4.8 33.2 1.0
MG B:MG402 4.8 30.9 1.0
CE B:LYS264 4.9 36.7 1.0
C4 B:IPE405 4.9 48.7 1.0
N B:ASP251 4.9 32.3 1.0
CA B:ASP250 5.0 32.5 1.0

Magnesium binding site 7 out of 9 in 4dxj

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Magnesium binding site 7 out of 9 in the Crystal Structure of Trypanosome Cruzi Farnesyl Diphosphate Synthase in Complex with [2-(N-Propylamino)Ethane-1,1-Diyl]Bisphosphonic Acid and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Trypanosome Cruzi Farnesyl Diphosphate Synthase in Complex with [2-(N-Propylamino)Ethane-1,1-Diyl]Bisphosphonic Acid and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg401

b:35.3
occ:1.00
 O C:HOH539 1.9 38.0 1.0
O5 C:0M9404 2.0 31.8 1.0
OD1 C:ASP98 2.1 35.8 1.0
O C:HOH540 2.3 19.9 1.0
O C:HOH538 2.3 29.9 1.0
OD2 C:ASP102 2.5 28.5 1.0
P2 C:0M9404 3.1 34.8 1.0
CG C:ASP98 3.1 34.3 1.0
O4 C:0M9404 3.2 31.5 1.0
MG C:MG402 3.3 32.7 1.0
CG C:ASP102 3.4 32.0 1.0
OD2 C:ASP98 3.4 36.2 1.0
OD2 C:ASP170 3.5 34.2 1.0
OD1 C:ASP102 3.5 30.3 1.0
C9 C:0M9404 3.9 33.9 1.0
NE2 C:GLN167 4.0 27.9 1.0
CG C:ASP170 4.0 34.0 1.0
OE1 C:GLN167 4.1 30.7 1.0
OD1 C:ASP170 4.2 33.6 1.0
O C:HOH536 4.2 31.7 1.0
O6 C:0M9404 4.3 33.5 1.0
N1 C:0M9404 4.3 34.2 1.0
NZ C:LYS273 4.4 35.2 1.0
CB C:ASP98 4.5 32.6 1.0
CD C:GLN167 4.5 29.2 1.0
NZ C:LYS207 4.7 34.3 1.0
C8 C:0M9404 4.8 34.5 1.0
CB C:ASP102 4.8 33.3 1.0
O C:HOH537 4.8 27.1 1.0
CB C:ASP170 5.0 33.9 1.0

Magnesium binding site 8 out of 9 in 4dxj

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Magnesium binding site 8 out of 9 in the Crystal Structure of Trypanosome Cruzi Farnesyl Diphosphate Synthase in Complex with [2-(N-Propylamino)Ethane-1,1-Diyl]Bisphosphonic Acid and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Trypanosome Cruzi Farnesyl Diphosphate Synthase in Complex with [2-(N-Propylamino)Ethane-1,1-Diyl]Bisphosphonic Acid and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg402

b:32.7
occ:1.00
 O C:HOH537 1.9 27.1 1.0
OD2 C:ASP98 2.0 36.2 1.0
O C:HOH536 2.1 31.7 1.0
O3 C:0M9404 2.1 32.9 1.0
O5 C:0M9404 2.2 31.8 1.0
OD2 C:ASP102 2.3 28.5 1.0
C9 C:0M9404 2.9 33.9 1.0
CG C:ASP98 3.0 34.3 1.0
P1 C:0M9404 3.1 34.3 1.0
P2 C:0M9404 3.1 34.8 1.0
MG C:MG401 3.3 35.3 1.0
OD1 C:ASP98 3.3 35.8 1.0
CG C:ASP102 3.4 32.0 1.0
O6 C:0M9404 3.8 33.5 1.0
O2 C:0M9404 3.9 34.2 1.0
CB C:ASP102 3.9 33.3 1.0
O C:HOH542 4.0 25.0 1.0
O C:HOH535 4.1 24.0 1.0
O C:HOH540 4.2 19.9 1.0
C8 C:0M9404 4.3 34.5 1.0
O1 C:0M9404 4.4 33.1 1.0
CB C:ASP98 4.4 32.6 1.0
O4 C:0M9404 4.4 31.5 1.0
OD1 C:ASP99 4.5 33.0 1.0
N1 C:0M9404 4.5 34.2 1.0
OD1 C:ASP102 4.5 30.3 1.0
OG C:SER104 4.6 37.1 1.0
O C:ASP98 4.6 32.3 1.0
NH1 C:ARG107 4.7 37.1 1.0
C C:ASP98 4.8 32.5 1.0
O C:HOH539 4.9 38.0 1.0
MG C:MG403 4.9 35.3 1.0

Magnesium binding site 9 out of 9 in 4dxj

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Magnesium binding site 9 out of 9 in the Crystal Structure of Trypanosome Cruzi Farnesyl Diphosphate Synthase in Complex with [2-(N-Propylamino)Ethane-1,1-Diyl]Bisphosphonic Acid and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of Trypanosome Cruzi Farnesyl Diphosphate Synthase in Complex with [2-(N-Propylamino)Ethane-1,1-Diyl]Bisphosphonic Acid and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg403

b:35.3
occ:1.00
 O6 C:0M9404 2.0 33.5 1.0
O2 C:0M9404 2.0 34.2 1.0
OD2 C:ASP250 2.2 35.6 1.0
O C:HOH534 2.3 23.4 1.0
O C:HOH535 2.3 24.0 1.0
O C:HOH533 2.4 29.0 1.0
CG C:ASP250 3.2 37.9 1.0
P2 C:0M9404 3.4 34.8 1.0
P1 C:0M9404 3.4 34.3 1.0
OD1 C:ASP250 3.7 39.0 1.0
C9 C:0M9404 4.0 33.9 1.0
NZ C:LYS264 4.0 43.3 1.0
O C:ASP250 4.1 38.6 1.0
NE2 C:GLN247 4.1 33.4 1.0
OD2 C:ASP268 4.1 40.5 1.0
OD1 C:ASP254 4.2 44.3 1.0
O5 C:0M9404 4.3 31.8 1.0
O3 C:0M9404 4.3 32.9 1.0
CB C:ASP250 4.3 37.7 1.0
O C:HOH536 4.3 31.7 1.0
OD1 C:ASP268 4.3 39.0 1.0
C C:ASP250 4.4 38.3 1.0
O4 C:0M9404 4.4 31.5 1.0
O1 C:0M9404 4.5 33.1 1.0
OD1 C:ASP251 4.5 39.6 1.0
CB C:ASP254 4.6 43.2 1.0
CG C:ASP268 4.7 40.6 1.0
CG C:ASP254 4.8 43.5 1.0
CE C:LYS264 4.8 42.8 1.0
N C:ASP251 4.8 38.6 1.0
C8 C:0M9404 4.9 34.5 1.0
O C:HOH542 4.9 25.0 1.0
MG C:MG402 4.9 32.7 1.0
CA C:ASP250 5.0 38.0 1.0

Reference:

S.Aripirala, S.H.Szajnman, J.Jakoncic, J.B.Rodriguez, R.Docampo, S.B.Gabelli, L.M.Amzel. Design, Synthesis, Calorimetry, and Crystallographic Analysis of 2-Alkylaminoethyl-1,1-Bisphosphonates As Inhibitors of Trypanosoma Cruzi Farnesyl Diphosphate Synthase. J.Med.Chem. V. 55 6445 2012.
ISSN: ISSN 0022-2623
PubMed: 22715997
DOI: 10.1021/JM300425Y
Page generated: Fri Aug 16 13:29:07 2024

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