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Calcium in PDB 3vry: Crystal Structure of Hck Complexed with A Pyrrolo-Pyrimidine Inhibitor 4-Amino-5-(4-Phenoxyphenyl)-7H-Pyrrolo[2,3-D]Pyrimidin-7-Yl- Cyclopentane

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

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

Protein crystallography data

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

Resolution Low / High (Å) 40.75 / 2.48
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 48.590, 73.880, 178.470, 90.00, 95.84, 90.00
R / Rfree (%) 22.6 / 28.1

Other elements in 3vry:

The structure of Crystal Structure of Hck Complexed with A Pyrrolo-Pyrimidine Inhibitor 4-Amino-5-(4-Phenoxyphenyl)-7H-Pyrrolo[2,3-D]Pyrimidin-7-Yl- Cyclopentane 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 4-Amino-5-(4-Phenoxyphenyl)-7H-Pyrrolo[2,3-D]Pyrimidin-7-Yl- Cyclopentane (pdb code 3vry). 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 4-Amino-5-(4-Phenoxyphenyl)-7H-Pyrrolo[2,3-D]Pyrimidin-7-Yl- Cyclopentane, PDB code: 3vry:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 3vry

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


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 4-Amino-5-(4-Phenoxyphenyl)-7H-Pyrrolo[2,3-D]Pyrimidin-7-Yl- Cyclopentane within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca603

b:43.8
occ:1.00
 O B:GLU524 2.7 24.6 1.0
OE2 A:GLU490 2.8 30.9 1.0
O A:HOH702 2.9 39.8 1.0
OE1 A:GLU490 3.1 29.3 1.0
O B:PTR527 3.1 37.4 1.0
CD A:GLU490 3.3 34.0 1.0
C B:GLU524 3.8 25.3 1.0
O A:HOH739 3.9 38.2 1.0
C B:PTR527 3.9 37.3 1.0
OE2 B:GLU524 3.9 42.7 1.0
CD B:GLU524 4.2 35.1 1.0
CG B:GLU529 4.3 61.7 1.0
N B:GLU529 4.5 44.2 1.0
N B:PTR527 4.5 28.6 1.0
OE2 B:GLU529 4.5 65.3 1.0
CA B:PTR527 4.6 33.1 1.0
CG B:GLU524 4.6 32.1 1.0
CA B:GLU524 4.6 28.8 1.0
N B:GLU528 4.6 39.0 1.0
CA B:GLU528 4.7 35.9 1.0
OE1 B:GLU524 4.7 33.7 1.0
N B:SER525 4.7 21.5 1.0
C B:GLU528 4.7 40.3 1.0
CA B:SER525 4.8 32.1 1.0
CD B:GLU529 4.8 73.0 1.0
CB B:GLU529 4.8 57.3 1.0
CG A:GLU490 4.8 30.3 1.0
CB B:PTR527 4.9 31.1 1.0
CB A:PRO488 4.9 32.7 1.0

Calcium binding site 2 out of 2 in 3vry

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


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 4-Amino-5-(4-Phenoxyphenyl)-7H-Pyrrolo[2,3-D]Pyrimidin-7-Yl- Cyclopentane within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca601

b:57.4
occ:1.00
 O A:GLU524 2.8 39.7 1.0
OE1 B:GLU490 2.9 40.4 1.0
OE2 B:GLU490 3.0 37.6 1.0
O A:PTR527 3.0 61.5 1.0
O B:HOH793 3.1 48.5 1.0
CD B:GLU490 3.3 43.4 1.0
C A:PTR527 3.7 55.0 1.0
CG A:GLU529 3.9 74.8 1.0
C A:GLU524 4.0 38.5 1.0
OE2 A:GLU524 4.1 40.7 1.0
C A:GLU528 4.2 65.2 1.0
O A:GLU528 4.2 63.1 1.0
N A:GLU528 4.4 61.9 1.0
CD A:GLU524 4.5 45.6 1.0
CA A:GLU528 4.5 60.3 1.0
N A:GLU529 4.5 69.4 1.0
CA A:PTR527 4.5 50.7 1.0
CD A:GLU529 4.6 75.8 1.0
OE2 A:GLU529 4.6 66.5 1.0
CG A:GLU524 4.6 37.4 1.0
N A:PTR527 4.6 50.5 1.0
CB B:PRO488 4.7 43.4 1.0
CB A:PTR527 4.7 43.3 1.0
CA A:GLU524 4.7 34.4 1.0
N B:GLU489 4.8 35.5 1.0
CG B:GLU490 4.9 35.9 1.0
N A:SER525 5.0 29.2 1.0
CB A:GLU529 5.0 72.7 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 20:50:06 2024

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