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Calcium in PDB 3vs6: Crystal Structure of Hck Complexed with A Pyrazolo-Pyrimidine Inhibitor Tert-Butyl {4-[4-Amino-1-(Propan-2-Yl)-1H-Pyrazolo[3,4- D]Pyrimidin-3-Yl]-2-Methoxyphenyl}Carbamate

Enzymatic activity of Crystal Structure of Hck Complexed with A Pyrazolo-Pyrimidine Inhibitor Tert-Butyl {4-[4-Amino-1-(Propan-2-Yl)-1H-Pyrazolo[3,4- D]Pyrimidin-3-Yl]-2-Methoxyphenyl}Carbamate

All present enzymatic activity of Crystal Structure of Hck Complexed with A Pyrazolo-Pyrimidine Inhibitor Tert-Butyl {4-[4-Amino-1-(Propan-2-Yl)-1H-Pyrazolo[3,4- D]Pyrimidin-3-Yl]-2-Methoxyphenyl}Carbamate:
2.7.10.2;

Protein crystallography data

The structure of Crystal Structure of Hck Complexed with A Pyrazolo-Pyrimidine Inhibitor Tert-Butyl {4-[4-Amino-1-(Propan-2-Yl)-1H-Pyrazolo[3,4- D]Pyrimidin-3-Yl]-2-Methoxyphenyl}Carbamate, PDB code: 3vs6 was solved by M.Kuratani, K.Honda, Y.Tomabechi, M.Toyama, N.Handa, S.Yokoyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.09 / 2.37
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.613, 96.392, 182.125, 90.00, 90.00, 90.00
R / Rfree (%) 23 / 28

Other elements in 3vs6:

The structure of Crystal Structure of Hck Complexed with A Pyrazolo-Pyrimidine Inhibitor Tert-Butyl {4-[4-Amino-1-(Propan-2-Yl)-1H-Pyrazolo[3,4- D]Pyrimidin-3-Yl]-2-Methoxyphenyl}Carbamate also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Hck Complexed with A Pyrazolo-Pyrimidine Inhibitor Tert-Butyl {4-[4-Amino-1-(Propan-2-Yl)-1H-Pyrazolo[3,4- D]Pyrimidin-3-Yl]-2-Methoxyphenyl}Carbamate (pdb code 3vs6). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Hck Complexed with A Pyrazolo-Pyrimidine Inhibitor Tert-Butyl {4-[4-Amino-1-(Propan-2-Yl)-1H-Pyrazolo[3,4- D]Pyrimidin-3-Yl]-2-Methoxyphenyl}Carbamate, PDB code: 3vs6:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3vs6

Go back to Calcium Binding Sites List in 3vs6
Calcium binding site 1 out of 4 in the Crystal Structure of Hck Complexed with A Pyrazolo-Pyrimidine Inhibitor Tert-Butyl {4-[4-Amino-1-(Propan-2-Yl)-1H-Pyrazolo[3,4- D]Pyrimidin-3-Yl]-2-Methoxyphenyl}Carbamate


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 Hck Complexed with A Pyrazolo-Pyrimidine Inhibitor Tert-Butyl {4-[4-Amino-1-(Propan-2-Yl)-1H-Pyrazolo[3,4- D]Pyrimidin-3-Yl]-2-Methoxyphenyl}Carbamate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca601

b:66.0
occ:1.00
 O A:GLU524 2.8 50.1 1.0
O A:PTR527 3.0 67.3 1.0
O A:HOH745 3.0 55.7 1.0
O A:HOH825 3.0 57.6 1.0
OE2 B:GLU490 3.0 60.9 1.0
OE1 B:GLU490 3.0 51.5 1.0
OE2 A:GLU529 3.1 90.4 1.0
OE1 A:GLU529 3.3 95.4 1.0
CD B:GLU490 3.4 66.5 1.0
CD A:GLU529 3.5 0.8 1.0
C A:PTR527 3.6 66.2 1.0
C A:GLU524 4.0 45.7 1.0
N A:PTR527 4.2 42.8 1.0
CA A:PTR527 4.3 59.9 1.0
N A:GLU528 4.3 69.9 1.0
CA A:GLU528 4.5 72.8 1.0
N A:GLU529 4.6 82.7 1.0
CB A:PTR527 4.6 48.9 1.0
OE2 A:GLU524 4.6 64.2 1.0
C A:GLU528 4.7 72.0 1.0
CD A:GLU524 4.8 74.8 1.0
CG A:GLU529 4.8 0.9 1.0
CG A:GLU524 4.8 66.1 1.0
CA A:GLU524 4.8 58.0 1.0
CA A:SER525 4.8 58.9 1.0
N A:SER525 4.9 32.7 1.0
N B:GLU489 4.9 59.8 1.0
CG B:GLU490 4.9 63.0 1.0
N A:GLN526 5.0 50.6 1.0
C A:SER525 5.0 62.6 1.0

Calcium binding site 2 out of 4 in 3vs6

Go back to Calcium Binding Sites List in 3vs6
Calcium binding site 2 out of 4 in the Crystal Structure of Hck Complexed with A Pyrazolo-Pyrimidine Inhibitor Tert-Butyl {4-[4-Amino-1-(Propan-2-Yl)-1H-Pyrazolo[3,4- D]Pyrimidin-3-Yl]-2-Methoxyphenyl}Carbamate


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 Hck Complexed with A Pyrazolo-Pyrimidine Inhibitor Tert-Butyl {4-[4-Amino-1-(Propan-2-Yl)-1H-Pyrazolo[3,4- D]Pyrimidin-3-Yl]-2-Methoxyphenyl}Carbamate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca604

b:0.7
occ:1.00
 OE2 B:GLU505 4.1 95.9 1.0
O B:GLU504 4.4 74.3 1.0
OE2 A:GLU510 4.8 77.8 1.0
OE1 A:GLU510 4.8 79.5 1.0
CD B:GLU505 4.9 0.1 1.0
OE1 A:GLN379 5.0 94.5 1.0

Calcium binding site 3 out of 4 in 3vs6

Go back to Calcium Binding Sites List in 3vs6
Calcium binding site 3 out of 4 in the Crystal Structure of Hck Complexed with A Pyrazolo-Pyrimidine Inhibitor Tert-Butyl {4-[4-Amino-1-(Propan-2-Yl)-1H-Pyrazolo[3,4- D]Pyrimidin-3-Yl]-2-Methoxyphenyl}Carbamate


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 Hck Complexed with A Pyrazolo-Pyrimidine Inhibitor Tert-Butyl {4-[4-Amino-1-(Propan-2-Yl)-1H-Pyrazolo[3,4- D]Pyrimidin-3-Yl]-2-Methoxyphenyl}Carbamate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca601

b:0.2
occ:1.00
 O B:HOH800 3.3 78.6 1.0
OE2 A:GLU505 3.5 0.4 1.0
OE1 B:GLN379 4.2 79.2 1.0
OE2 B:GLU510 4.3 79.9 1.0
NE2 B:GLN379 4.4 95.9 1.0
CD B:GLN379 4.7 87.1 1.0
CD A:GLU505 4.8 0.7 1.0
O A:GLU504 4.8 64.5 1.0
OE1 B:GLU510 4.9 77.2 1.0
CD B:GLU510 5.0 77.1 1.0

Calcium binding site 4 out of 4 in 3vs6

Go back to Calcium Binding Sites List in 3vs6
Calcium binding site 4 out of 4 in the Crystal Structure of Hck Complexed with A Pyrazolo-Pyrimidine Inhibitor Tert-Butyl {4-[4-Amino-1-(Propan-2-Yl)-1H-Pyrazolo[3,4- D]Pyrimidin-3-Yl]-2-Methoxyphenyl}Carbamate


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 Hck Complexed with A Pyrazolo-Pyrimidine Inhibitor Tert-Butyl {4-[4-Amino-1-(Propan-2-Yl)-1H-Pyrazolo[3,4- D]Pyrimidin-3-Yl]-2-Methoxyphenyl}Carbamate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca604

b:84.2
occ:1.00
 O B:GLU524 3.0 56.8 1.0
O B:PTR527 3.0 69.6 1.0
OE2 A:GLU490 3.0 58.1 1.0
O B:HOH807 3.0 69.9 1.0
OE1 A:GLU490 3.1 59.4 1.0
O A:HOH742 3.4 66.8 1.0
CD A:GLU490 3.4 63.6 1.0
C B:PTR527 3.5 70.4 1.0
O B:HOH811 3.6 70.2 1.0
C B:GLU528 3.9 85.8 1.0
N B:GLU528 4.0 79.2 1.0
O B:GLU528 4.1 81.5 1.0
N B:GLU529 4.1 0.4 1.0
CG B:GLU529 4.1 0.2 1.0
CA B:GLU528 4.1 79.0 1.0
C B:GLU524 4.2 52.2 1.0
OE2 B:GLU524 4.3 58.2 1.0
CA B:PTR527 4.3 65.9 1.0
N B:PTR527 4.4 66.7 1.0
CB B:PTR527 4.6 65.0 1.0
N A:GLU489 4.7 51.3 1.0
CA B:GLU529 4.7 0.2 1.0
CB A:GLU489 4.7 59.6 1.0
CD B:GLU524 4.8 68.3 1.0
CB B:GLU529 4.8 0.8 1.0
CD B:GLU529 4.9 0.8 1.0
CG A:GLU490 5.0 56.1 1.0
CG B:GLU524 5.0 63.0 1.0

Reference:

Y.Saito, H.Yuki, M.Kuratani, Y.Hashizume, S.Takagi, T.Honma, A.Tanaka, M.Shirouzu, J.Mikuni, N.Handa, I.Ogahara, A.Sone, Y.Najima, Y.Tomabechi, M.Wakiyama, N.Uchida, M.Tomizawa-Murasawa, A.Kaneko, S.Tanaka, N.Suzuki, H.Kajita, Y.Aoki, O.Ohara, L.D.Shultz, T.Fukami, T.Goto, S.Taniguchi, S.Yokoyama, F.Ishikawa. A Pyrrolo-Pyrimidine Derivative Targets Human Primary Aml Stem Cells in Vivo Sci Transl Med V. 5 1RA52 2013.
ISSN: ISSN 1946-6234
PubMed: 23596204
DOI: 10.1126/SCITRANSLMED.3004387
Page generated: Sat Jul 13 20:51:40 2024

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