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Calcium in PDB 3vs3: Crystal Structure of Hck Complexed with A Pyrrolo-Pyrimidine Inhibitor 7-[Trans-4-(4-Methylpiperazin-1-Yl)Cyclohexyl]-5-(4-Phenoxyphenyl)- 7H-Pyrrolo[2,3-D]Pyrimidin-4-Amine

Enzymatic activity of Crystal Structure of Hck Complexed with A Pyrrolo-Pyrimidine Inhibitor 7-[Trans-4-(4-Methylpiperazin-1-Yl)Cyclohexyl]-5-(4-Phenoxyphenyl)- 7H-Pyrrolo[2,3-D]Pyrimidin-4-Amine

All present enzymatic activity of Crystal Structure of Hck Complexed with A Pyrrolo-Pyrimidine Inhibitor 7-[Trans-4-(4-Methylpiperazin-1-Yl)Cyclohexyl]-5-(4-Phenoxyphenyl)- 7H-Pyrrolo[2,3-D]Pyrimidin-4-Amine:
2.7.10.2;

Protein crystallography data

The structure of Crystal Structure of Hck Complexed with A Pyrrolo-Pyrimidine Inhibitor 7-[Trans-4-(4-Methylpiperazin-1-Yl)Cyclohexyl]-5-(4-Phenoxyphenyl)- 7H-Pyrrolo[2,3-D]Pyrimidin-4-Amine, PDB code: 3vs3 was solved by M.Kuratani, Y.Tomaebchi, N.Handa, S.Yokoyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.46 / 2.17
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 48.450, 73.592, 180.712, 90.00, 96.30, 90.00
R / Rfree (%) 22.6 / 27.9

Other elements in 3vs3:

The structure of Crystal Structure of Hck Complexed with A Pyrrolo-Pyrimidine Inhibitor 7-[Trans-4-(4-Methylpiperazin-1-Yl)Cyclohexyl]-5-(4-Phenoxyphenyl)- 7H-Pyrrolo[2,3-D]Pyrimidin-4-Amine 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 Pyrrolo-Pyrimidine Inhibitor 7-[Trans-4-(4-Methylpiperazin-1-Yl)Cyclohexyl]-5-(4-Phenoxyphenyl)- 7H-Pyrrolo[2,3-D]Pyrimidin-4-Amine (pdb code 3vs3). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Hck Complexed with A Pyrrolo-Pyrimidine Inhibitor 7-[Trans-4-(4-Methylpiperazin-1-Yl)Cyclohexyl]-5-(4-Phenoxyphenyl)- 7H-Pyrrolo[2,3-D]Pyrimidin-4-Amine, PDB code: 3vs3:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 3vs3

Go back to Calcium Binding Sites List in 3vs3
Calcium binding site 1 out of 2 in the Crystal Structure of Hck Complexed with A Pyrrolo-Pyrimidine Inhibitor 7-[Trans-4-(4-Methylpiperazin-1-Yl)Cyclohexyl]-5-(4-Phenoxyphenyl)- 7H-Pyrrolo[2,3-D]Pyrimidin-4-Amine


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 Pyrrolo-Pyrimidine Inhibitor 7-[Trans-4-(4-Methylpiperazin-1-Yl)Cyclohexyl]-5-(4-Phenoxyphenyl)- 7H-Pyrrolo[2,3-D]Pyrimidin-4-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca602

b:52.6
occ:1.00
 O A:PTR527 2.9 34.5 1.0
O A:GLU524 2.9 39.4 1.0
OE1 B:GLU490 3.0 35.8 1.0
OE2 A:GLU529 3.0 62.4 1.0
OE2 B:GLU490 3.1 38.9 1.0
O A:HOH726 3.2 38.9 1.0
CD B:GLU490 3.4 46.5 1.0
C A:PTR527 3.8 37.4 1.0
C A:GLU524 4.0 30.6 1.0
CD A:GLU529 4.1 70.6 1.0
OE2 A:GLU524 4.2 61.7 1.0
N A:PTR527 4.4 30.7 1.0
CA A:PTR527 4.5 36.2 1.0
N A:GLU528 4.6 47.7 1.0
N A:GLU529 4.6 53.2 1.0
CD A:GLU524 4.6 50.3 1.0
CA A:GLU528 4.7 38.5 1.0
CB A:PTR527 4.7 37.3 1.0
N B:GLU489 4.8 39.6 1.0
CB A:GLU529 4.8 63.6 1.0
OE1 A:GLU529 4.8 64.0 1.0
CG A:GLU524 4.8 49.7 1.0
CA A:GLU524 4.8 38.8 1.0
C A:GLU528 4.8 47.0 1.0
N A:SER525 4.9 27.0 1.0
O A:HOH829 4.9 57.1 1.0
CG B:GLU490 4.9 37.9 1.0
CA A:SER525 4.9 34.4 1.0

Calcium binding site 2 out of 2 in 3vs3

Go back to Calcium Binding Sites List in 3vs3
Calcium binding site 2 out of 2 in the Crystal Structure of Hck Complexed with A Pyrrolo-Pyrimidine Inhibitor 7-[Trans-4-(4-Methylpiperazin-1-Yl)Cyclohexyl]-5-(4-Phenoxyphenyl)- 7H-Pyrrolo[2,3-D]Pyrimidin-4-Amine


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 Pyrrolo-Pyrimidine Inhibitor 7-[Trans-4-(4-Methylpiperazin-1-Yl)Cyclohexyl]-5-(4-Phenoxyphenyl)- 7H-Pyrrolo[2,3-D]Pyrimidin-4-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca602

b:74.9
occ:1.00
 O B:PTR527 3.0 62.7 1.0
O B:GLU524 3.0 39.5 1.0
OE1 A:GLU490 3.1 45.6 1.0
O B:HOH859 3.1 63.3 1.0
OE2 A:GLU490 3.1 42.6 1.0
O B:HOH719 3.2 48.9 1.0
O A:HOH721 3.2 59.5 1.0
CD A:GLU490 3.5 47.8 1.0
C B:PTR527 3.6 67.6 1.0
C B:GLU528 4.2 72.6 1.0
N B:GLU528 4.2 72.5 1.0
OE2 B:GLU524 4.2 67.5 1.0
C B:GLU524 4.2 36.4 1.0
CA B:PTR527 4.3 62.3 1.0
O B:GLU528 4.3 71.6 1.0
CG B:GLU529 4.3 99.4 1.0
CA B:GLU528 4.4 65.6 1.0
N B:PTR527 4.4 61.2 1.0
CB B:PTR527 4.4 50.9 1.0
N B:GLU529 4.5 80.2 1.0
N A:GLU489 4.7 50.5 1.0
CD B:GLU524 4.8 60.9 1.0
CB A:PRO488 4.9 49.2 1.0
CB A:GLU489 5.0 46.7 1.0
CG A:GLU490 5.0 40.6 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 20:51:22 2024

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