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Calcium in PDB 2aei: Crystal Structure of A Ternary Complex of Factor Viia/Tissue Factor and 2-[[6-[3-(Aminoiminomethyl)Phenoxy]-3,5-Difluro-4-[(1-Methyl-3- Phenylpropyl)Amino]-2-Pyridinyl]Oxy]-Benzoic Acid

Enzymatic activity of Crystal Structure of A Ternary Complex of Factor Viia/Tissue Factor and 2-[[6-[3-(Aminoiminomethyl)Phenoxy]-3,5-Difluro-4-[(1-Methyl-3- Phenylpropyl)Amino]-2-Pyridinyl]Oxy]-Benzoic Acid

All present enzymatic activity of Crystal Structure of A Ternary Complex of Factor Viia/Tissue Factor and 2-[[6-[3-(Aminoiminomethyl)Phenoxy]-3,5-Difluro-4-[(1-Methyl-3- Phenylpropyl)Amino]-2-Pyridinyl]Oxy]-Benzoic Acid:
3.4.21.21;

Protein crystallography data

The structure of Crystal Structure of A Ternary Complex of Factor Viia/Tissue Factor and 2-[[6-[3-(Aminoiminomethyl)Phenoxy]-3,5-Difluro-4-[(1-Methyl-3- Phenylpropyl)Amino]-2-Pyridinyl]Oxy]-Benzoic Acid, PDB code: 2aei was solved by M.Adler, M.Whitlow, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.52
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 70.215, 80.496, 125.936, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / 29.7

Other elements in 2aei:

The structure of Crystal Structure of A Ternary Complex of Factor Viia/Tissue Factor and 2-[[6-[3-(Aminoiminomethyl)Phenoxy]-3,5-Difluro-4-[(1-Methyl-3- Phenylpropyl)Amino]-2-Pyridinyl]Oxy]-Benzoic Acid also contains other interesting chemical elements:

Fluorine (F) 2 atoms
Arsenic (As) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of A Ternary Complex of Factor Viia/Tissue Factor and 2-[[6-[3-(Aminoiminomethyl)Phenoxy]-3,5-Difluro-4-[(1-Methyl-3- Phenylpropyl)Amino]-2-Pyridinyl]Oxy]-Benzoic Acid (pdb code 2aei). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of A Ternary Complex of Factor Viia/Tissue Factor and 2-[[6-[3-(Aminoiminomethyl)Phenoxy]-3,5-Difluro-4-[(1-Methyl-3- Phenylpropyl)Amino]-2-Pyridinyl]Oxy]-Benzoic Acid, PDB code: 2aei:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 2aei

Go back to Calcium Binding Sites List in 2aei
Calcium binding site 1 out of 8 in the Crystal Structure of A Ternary Complex of Factor Viia/Tissue Factor and 2-[[6-[3-(Aminoiminomethyl)Phenoxy]-3,5-Difluro-4-[(1-Methyl-3- Phenylpropyl)Amino]-2-Pyridinyl]Oxy]-Benzoic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of A Ternary Complex of Factor Viia/Tissue Factor and 2-[[6-[3-(Aminoiminomethyl)Phenoxy]-3,5-Difluro-4-[(1-Methyl-3- Phenylpropyl)Amino]-2-Pyridinyl]Oxy]-Benzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca501

b:72.1
occ:1.00
 OE12 L:CGU29 1.7 57.6 1.0
OE12 L:CGU25 1.7 66.7 1.0
OE21 L:CGU25 1.8 67.4 1.0
CD1 L:CGU25 2.6 61.4 1.0
CD1 L:CGU29 2.6 53.5 1.0
CD2 L:CGU25 2.6 63.5 1.0
CG L:CGU25 2.9 58.5 1.0
OE11 L:CGU29 3.1 57.7 1.0
OE22 L:CGU29 3.5 39.7 1.0
OE11 L:CGU25 3.7 61.0 1.0
OE22 L:CGU25 3.8 63.7 1.0
CG L:CGU29 3.8 48.5 1.0
NH2 L:ARG28 4.1 65.0 1.0
CD2 L:CGU29 4.1 46.9 1.0
CA L:CA502 4.3 79.2 1.0
CB L:CGU25 4.4 52.4 1.0
CB L:CGU29 4.5 48.8 1.0
O L:CGU25 4.9 43.7 1.0

Calcium binding site 2 out of 8 in 2aei

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Calcium binding site 2 out of 8 in the Crystal Structure of A Ternary Complex of Factor Viia/Tissue Factor and 2-[[6-[3-(Aminoiminomethyl)Phenoxy]-3,5-Difluro-4-[(1-Methyl-3- Phenylpropyl)Amino]-2-Pyridinyl]Oxy]-Benzoic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of A Ternary Complex of Factor Viia/Tissue Factor and 2-[[6-[3-(Aminoiminomethyl)Phenoxy]-3,5-Difluro-4-[(1-Methyl-3- Phenylpropyl)Amino]-2-Pyridinyl]Oxy]-Benzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca502

b:79.2
occ:1.00
 OE12 L:CGU7 1.7 57.0 1.0
OE11 L:CGU26 1.7 57.9 1.0
OE22 L:CGU29 1.7 39.7 1.0
CD1 L:CGU7 2.3 56.1 1.0
CD2 L:CGU29 2.8 46.9 1.0
OE11 L:CGU7 2.8 53.5 1.0
CD1 L:CGU26 2.9 56.9 1.0
OE21 L:CGU29 3.2 49.4 1.0
OE21 L:CGU7 3.3 55.5 1.0
OE21 L:CGU25 3.3 67.4 1.0
CD2 L:CGU7 3.3 56.2 1.0
CG L:CGU7 3.4 54.8 1.0
OE12 L:CGU26 3.5 64.7 1.0
CD2 L:CGU25 3.8 63.5 1.0
OE12 L:CGU29 3.8 57.6 1.0
ND2 L:ASN2 3.8 32.8 1.0
CG L:CGU26 4.0 49.8 1.0
OE22 L:CGU7 4.0 55.6 1.0
CA L:CA503 4.1 54.0 1.0
CG L:CGU29 4.1 48.5 1.0
OE22 L:CGU25 4.2 63.7 1.0
OD1 L:ASN2 4.3 33.6 1.0
CA L:CA501 4.3 72.1 1.0
CG L:ASN2 4.4 31.9 1.0
CD1 L:CGU29 4.4 53.5 1.0
CB L:CGU7 4.5 54.3 1.0
CG L:CGU25 4.5 58.5 1.0
CA L:CGU26 4.8 41.8 1.0

Calcium binding site 3 out of 8 in 2aei

Go back to Calcium Binding Sites List in 2aei
Calcium binding site 3 out of 8 in the Crystal Structure of A Ternary Complex of Factor Viia/Tissue Factor and 2-[[6-[3-(Aminoiminomethyl)Phenoxy]-3,5-Difluro-4-[(1-Methyl-3- Phenylpropyl)Amino]-2-Pyridinyl]Oxy]-Benzoic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of A Ternary Complex of Factor Viia/Tissue Factor and 2-[[6-[3-(Aminoiminomethyl)Phenoxy]-3,5-Difluro-4-[(1-Methyl-3- Phenylpropyl)Amino]-2-Pyridinyl]Oxy]-Benzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca503

b:54.0
occ:1.00
 OE21 L:CGU29 1.8 49.4 1.0
OE21 L:CGU7 1.8 55.5 1.0
OE22 L:CGU7 1.9 55.6 1.0
OE12 L:CGU16 1.9 38.6 1.0
CD2 L:CGU7 2.2 56.2 1.0
CD1 L:CGU16 2.9 38.7 1.0
CD2 L:CGU29 3.0 46.9 1.0
OE11 L:CGU16 3.1 41.8 1.0
CA L:CA504 3.5 38.7 1.0
CG L:CGU26 3.6 49.8 1.0
OE11 L:CGU26 3.6 57.9 1.0
OE22 L:CGU29 3.7 39.7 1.0
CG L:CGU7 3.7 54.8 1.0
OE11 L:CGU6 3.9 66.1 1.0
OE21 L:CGU26 4.0 50.9 1.0
CD1 L:CGU26 4.1 56.9 1.0
CA L:CA502 4.1 79.2 1.0
CG L:CGU29 4.2 48.5 1.0
CG L:CGU16 4.3 39.4 1.0
CD2 L:CGU26 4.3 48.1 1.0
OE21 L:CGU16 4.4 38.5 1.0
OE12 L:CGU7 4.4 57.0 1.0
CB L:CGU26 4.4 42.4 1.0
CA L:GLY11 4.4 45.4 1.0
CD1 L:CGU7 4.4 56.1 1.0
OE12 L:CGU6 4.5 63.0 1.0
OD1 L:ASN2 4.5 33.6 1.0
CA L:CGU26 4.6 41.8 1.0
CB L:CGU29 4.6 48.8 1.0
O L:CGU26 4.6 43.6 1.0
CB L:CGU7 4.6 54.3 1.0
CD1 L:CGU6 4.6 66.2 1.0
CD2 L:CGU16 4.8 44.0 1.0
N L:GLY11 4.8 46.0 1.0
CA L:CGU7 4.9 54.1 1.0

Calcium binding site 4 out of 8 in 2aei

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Calcium binding site 4 out of 8 in the Crystal Structure of A Ternary Complex of Factor Viia/Tissue Factor and 2-[[6-[3-(Aminoiminomethyl)Phenoxy]-3,5-Difluro-4-[(1-Methyl-3- Phenylpropyl)Amino]-2-Pyridinyl]Oxy]-Benzoic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of A Ternary Complex of Factor Viia/Tissue Factor and 2-[[6-[3-(Aminoiminomethyl)Phenoxy]-3,5-Difluro-4-[(1-Methyl-3- Phenylpropyl)Amino]-2-Pyridinyl]Oxy]-Benzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca504

b:38.7
occ:1.00
 OE21 L:CGU26 1.7 50.9 1.0
OE11 L:CGU6 1.7 66.1 1.0
OE21 L:CGU16 1.8 38.5 1.0
OD1 L:ASN2 2.3 33.6 1.0
OE12 L:CGU16 2.4 38.6 1.0
OE21 L:CGU7 2.4 55.5 1.0
O L:ALA1 2.6 38.6 1.0
CD1 L:CGU6 2.7 66.2 1.0
CD2 L:CGU26 2.9 48.1 1.0
CD2 L:CGU16 2.9 44.0 1.0
CD1 L:CGU16 3.3 38.7 1.0
OE12 L:CGU6 3.3 63.0 1.0
CD2 L:CGU7 3.3 56.2 1.0
CA L:CA503 3.5 54.0 1.0
CG L:CGU26 3.5 49.8 1.0
CG L:ASN2 3.5 31.9 1.0
C L:ALA1 3.6 38.8 1.0
CG L:CGU16 3.6 39.4 1.0
CA L:CA505 3.7 0.2 1.0
CG L:CGU6 3.8 65.8 1.0
OE22 L:CGU16 3.8 50.3 1.0
OE22 L:CGU26 3.9 46.3 1.0
CD2 L:CGU6 4.0 70.7 1.0
CA L:ASN2 4.0 37.0 1.0
CG L:CGU7 4.1 54.8 1.0
OE22 L:CGU7 4.1 55.6 1.0
OE11 L:CGU26 4.2 57.9 1.0
N L:ASN2 4.2 38.5 1.0
CD1 L:CGU26 4.2 56.9 1.0
OE21 L:CGU6 4.3 73.2 1.0
N L:ALA1 4.3 38.3 1.0
CB L:ASN2 4.4 31.0 1.0
OE22 L:CGU6 4.4 74.5 1.0
OE11 L:CGU16 4.4 41.8 1.0
ND2 L:ASN2 4.5 32.8 1.0
CB L:CGU16 4.5 38.3 1.0
CA L:ALA1 4.6 38.1 1.0
CB L:CGU26 4.8 42.4 1.0
OE21 L:CGU29 4.9 49.4 1.0
CD1 L:CGU7 4.9 56.1 1.0

Calcium binding site 5 out of 8 in 2aei

Go back to Calcium Binding Sites List in 2aei
Calcium binding site 5 out of 8 in the Crystal Structure of A Ternary Complex of Factor Viia/Tissue Factor and 2-[[6-[3-(Aminoiminomethyl)Phenoxy]-3,5-Difluro-4-[(1-Methyl-3- Phenylpropyl)Amino]-2-Pyridinyl]Oxy]-Benzoic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of A Ternary Complex of Factor Viia/Tissue Factor and 2-[[6-[3-(Aminoiminomethyl)Phenoxy]-3,5-Difluro-4-[(1-Methyl-3- Phenylpropyl)Amino]-2-Pyridinyl]Oxy]-Benzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca505

b:0.2
occ:1.00
 OE22 L:CGU6 1.7 74.5 1.0
OE21 L:CGU20 1.7 67.1 1.0
OE22 L:CGU16 1.7 50.3 1.0
OE21 L:CGU16 2.3 38.5 1.0
CD2 L:CGU16 2.3 44.0 1.0
CD2 L:CGU6 2.3 70.7 1.0
OE21 L:CGU6 2.7 73.2 1.0
O L:ALA1 2.9 38.6 1.0
CD2 L:CGU20 2.9 66.1 1.0
CD1 L:CGU6 3.4 66.2 1.0
CG L:CGU6 3.4 65.8 1.0
OE22 L:CGU20 3.5 66.8 1.0
OE12 L:CGU6 3.6 63.0 1.0
CA L:CA504 3.7 38.7 1.0
OE11 L:CGU6 3.7 66.1 1.0
CG L:CGU16 3.8 39.4 1.0
C L:ALA1 4.0 38.8 1.0
CG L:CGU20 4.1 65.8 1.0
NE L:ARG15 4.2 46.2 1.0
N L:ALA1 4.3 38.3 1.0
CA L:CGU16 4.3 38.6 1.0
CB L:CGU6 4.4 62.1 1.0
O L:ARG15 4.4 41.6 1.0
CB L:CGU20 4.5 59.2 1.0
CB L:CGU16 4.5 38.3 1.0
OE21 L:CGU26 4.5 50.9 1.0
CG L:ARG15 4.6 45.3 1.0
CA L:ALA1 4.7 38.1 1.0
N L:CGU16 4.8 37.9 1.0
C L:ARG15 4.8 40.8 1.0
CD L:ARG15 4.8 46.5 1.0
OE12 L:CGU16 4.8 38.6 1.0
CD1 L:CGU16 4.8 38.7 1.0
N L:ASN2 5.0 38.5 1.0

Calcium binding site 6 out of 8 in 2aei

Go back to Calcium Binding Sites List in 2aei
Calcium binding site 6 out of 8 in the Crystal Structure of A Ternary Complex of Factor Viia/Tissue Factor and 2-[[6-[3-(Aminoiminomethyl)Phenoxy]-3,5-Difluro-4-[(1-Methyl-3- Phenylpropyl)Amino]-2-Pyridinyl]Oxy]-Benzoic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of A Ternary Complex of Factor Viia/Tissue Factor and 2-[[6-[3-(Aminoiminomethyl)Phenoxy]-3,5-Difluro-4-[(1-Methyl-3- Phenylpropyl)Amino]-2-Pyridinyl]Oxy]-Benzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca506

b:86.2
occ:1.00
 OE12 L:CGU19 1.7 83.0 1.0
OE12 L:CGU20 1.7 77.5 1.0
OE22 L:CGU20 1.7 66.8 1.0
CD1 L:CGU20 2.7 72.1 1.0
CD2 L:CGU20 2.7 66.1 1.0
CD1 L:CGU19 2.9 76.8 1.0
CG L:CGU20 3.2 65.8 1.0
OE22 L:CGU19 3.5 77.6 1.0
OE11 L:CGU19 3.8 79.2 1.0
OE11 L:CGU20 3.8 76.0 1.0
OE21 L:CGU20 3.9 67.1 1.0
CG L:CGU19 3.9 71.5 1.0
O L:ARG15 4.0 41.6 1.0
CB L:CGU20 4.1 59.2 1.0
CD2 L:CGU19 4.2 74.5 1.0
CB L:CGU19 4.3 64.5 1.0
N L:CGU20 4.4 57.5 1.0
C L:CGU19 4.6 58.4 1.0
CA L:CGU20 4.7 56.7 1.0
CG L:ARG15 4.8 45.3 1.0
O L:CGU19 4.8 57.8 1.0
C L:ARG15 4.9 40.8 1.0

Calcium binding site 7 out of 8 in 2aei

Go back to Calcium Binding Sites List in 2aei
Calcium binding site 7 out of 8 in the Crystal Structure of A Ternary Complex of Factor Viia/Tissue Factor and 2-[[6-[3-(Aminoiminomethyl)Phenoxy]-3,5-Difluro-4-[(1-Methyl-3- Phenylpropyl)Amino]-2-Pyridinyl]Oxy]-Benzoic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of A Ternary Complex of Factor Viia/Tissue Factor and 2-[[6-[3-(Aminoiminomethyl)Phenoxy]-3,5-Difluro-4-[(1-Methyl-3- Phenylpropyl)Amino]-2-Pyridinyl]Oxy]-Benzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca509

b:51.4
occ:1.00
 O L:GLN64 1.7 38.6 1.0
O L:GLY47 1.9 47.3 1.0
OE1 L:GLN49 2.0 41.7 1.0
O L:ASP46 2.3 50.8 1.0
OD1 L:ASP63 2.7 37.2 1.0
OD2 L:ASP63 2.7 39.1 1.0
C L:GLN64 3.0 37.6 1.0
CG L:ASP63 3.1 36.3 1.0
C L:GLY47 3.1 46.8 1.0
CD L:GLN49 3.2 38.6 1.0
C L:ASP46 3.5 48.2 1.0
N L:GLN66 3.7 42.2 1.0
NE2 L:GLN49 3.7 37.6 1.0
N L:GLN64 3.8 38.0 1.0
N L:LEU65 3.9 37.9 1.0
CA L:LEU65 3.9 40.1 1.0
CA L:GLY47 4.1 44.8 1.0
CA L:GLN64 4.1 38.1 1.0
N L:ASP48 4.1 46.4 1.0
N L:GLY47 4.2 44.6 1.0
N L:GLN49 4.2 44.1 1.0
O L:SER67 4.3 25.9 1.0
CA L:ASP48 4.3 47.2 1.0
C L:LEU65 4.3 41.1 1.0
CG L:GLN49 4.5 38.0 1.0
CB L:ASP63 4.6 35.8 1.0
OE1 L:GLN66 4.6 40.4 0.2
CB L:ASP46 4.7 44.9 0.5
CA L:GLN66 4.7 40.7 1.0
CA L:ASP46 4.8 48.3 1.0
C L:ASP63 4.8 36.4 1.0
C L:ASP48 4.8 45.9 1.0
N L:SER67 4.8 35.5 1.0
CB L:GLN49 4.9 41.1 1.0

Calcium binding site 8 out of 8 in 2aei

Go back to Calcium Binding Sites List in 2aei
Calcium binding site 8 out of 8 in the Crystal Structure of A Ternary Complex of Factor Viia/Tissue Factor and 2-[[6-[3-(Aminoiminomethyl)Phenoxy]-3,5-Difluro-4-[(1-Methyl-3- Phenylpropyl)Amino]-2-Pyridinyl]Oxy]-Benzoic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of A Ternary Complex of Factor Viia/Tissue Factor and 2-[[6-[3-(Aminoiminomethyl)Phenoxy]-3,5-Difluro-4-[(1-Methyl-3- Phenylpropyl)Amino]-2-Pyridinyl]Oxy]-Benzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca510

b:32.3
occ:1.00
 O H:GLU75 1.6 46.7 1.0
O H:HOH632 1.7 20.2 1.0
O H:ASP72 2.2 12.3 1.0
OE2 H:GLU80 2.4 24.9 1.0
OE2 H:GLU70 2.5 21.6 1.0
C H:GLU75 2.9 46.8 1.0
CD H:GLU70 3.3 20.6 1.0
OE1 H:GLU70 3.3 31.1 1.0
C H:ASP72 3.4 13.1 1.0
CD H:GLU80 3.7 26.3 1.0
N H:HIS76 3.8 47.9 1.0
N H:GLU75 3.8 40.6 1.0
CA H:GLU75 3.8 46.1 1.0
CA H:HIS76 3.9 52.0 1.0
O H:HOH645 4.1 26.4 1.0
N H:ASP72 4.2 15.7 1.0
CA H:ASP72 4.2 14.0 1.0
N H:LEU73 4.4 11.3 1.0
OE1 H:GLU80 4.4 28.7 1.0
CB H:ASP72 4.4 21.1 1.0
CA H:LEU73 4.5 16.0 1.0
CB H:GLU75 4.6 52.7 1.0
N H:ASP77 4.6 50.9 1.0
C H:LEU73 4.7 21.5 1.0
CG H:GLU80 4.7 26.9 1.0
CG H:GLU70 4.7 9.2 1.0
OD2 H:ASP77 4.8 55.5 1.0
CG H:GLU75 4.8 63.9 1.0
C H:HIS76 4.9 49.7 1.0
N H:SER74 4.9 29.5 1.0
N H:HIS71 4.9 18.6 1.0
O H:LEU73 5.0 19.2 1.0
CB H:HIS76 5.0 56.7 1.0

Reference:

J.T.Kohrt, K.J.Filipski, W.L.Cody, C.Cai, D.A.Dudley, C.A.Van Huis, J.A.Willardsen, S.T.Rapundalo, K.Saiya-Cork, R.J.Leadley, L.Narasimhan, E.Zhang, M.Whitlow, M.Adler, K.Mclean, Y.L.Chou, C.Mcknight, D.O.Arnaiz, K.J.Shaw, D.R.Light, J.J.Edmunds. The Discovery of Fluoropyridine-Based Inhibitors of the Factor Viia/Tf Complex. Bioorg.Med.Chem.Lett. V. 15 4752 2005.
ISSN: ISSN 0960-894X
PubMed: 16125385
DOI: 10.1016/J.BMCL.2005.07.059
Page generated: Fri Jul 12 08:40:38 2024

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