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Calcium in PDB 3vrz: Crystal Structure of Hck Complexed with A Pyrrolo-Pyrimidine Inhibitor 1-[4-(4-Amino-7-Cyclopentyl-7H-Pyrrolo[2,3-D]Pyrimidin-5-Yl)Phenyl]- 3-Benzylurea

Enzymatic activity of Crystal Structure of Hck Complexed with A Pyrrolo-Pyrimidine Inhibitor 1-[4-(4-Amino-7-Cyclopentyl-7H-Pyrrolo[2,3-D]Pyrimidin-5-Yl)Phenyl]- 3-Benzylurea

All present enzymatic activity of Crystal Structure of Hck Complexed with A Pyrrolo-Pyrimidine Inhibitor 1-[4-(4-Amino-7-Cyclopentyl-7H-Pyrrolo[2,3-D]Pyrimidin-5-Yl)Phenyl]- 3-Benzylurea:
2.7.10.2;

Protein crystallography data

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

Resolution Low / High (Å) 49.14 / 2.22
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 73.645, 96.492, 180.864, 90.00, 90.00, 90.00
R / Rfree (%) 23.9 / 26.7

Other elements in 3vrz:

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

Calcium binding site 1 out of 2 in 3vrz

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


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 1-[4-(4-Amino-7-Cyclopentyl-7H-Pyrrolo[2,3-D]Pyrimidin-5-Yl)Phenyl]- 3-Benzylurea within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca601

b:42.0
occ:1.00
 O A:GLU524 2.7 29.9 1.0
O A:PTR527 2.8 41.7 1.0
O A:HOH715 3.0 57.6 1.0
O A:HOH720 3.2 57.0 1.0
O A:HOH719 3.6 60.3 1.0
C A:PTR527 3.7 41.6 1.0
C A:GLU524 3.8 31.6 1.0
N A:PTR527 4.1 32.0 1.0
CA A:PTR527 4.2 35.8 1.0
CG A:GLU529 4.3 68.4 1.0
CB A:PTR527 4.5 35.2 1.0
CA A:SER525 4.6 32.4 1.0
CD A:GLU524 4.6 36.2 1.0
C A:GLU528 4.6 49.2 1.0
OE2 A:GLU524 4.6 42.5 1.0
N A:GLU528 4.6 48.0 1.0
N A:SER525 4.6 26.2 1.0
O A:GLU528 4.6 40.7 1.0
CA A:GLU524 4.6 28.9 1.0
N A:GLN526 4.7 31.6 1.0
CG A:GLU524 4.7 33.6 1.0
C A:SER525 4.8 35.0 1.0
CA A:GLU528 4.8 44.8 1.0
N A:GLU529 4.9 51.6 1.0
OE1 A:GLU524 4.9 33.8 1.0

Calcium binding site 2 out of 2 in 3vrz

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


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 1-[4-(4-Amino-7-Cyclopentyl-7H-Pyrrolo[2,3-D]Pyrimidin-5-Yl)Phenyl]- 3-Benzylurea within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca601

b:45.6
occ:1.00
 O B:GLU524 2.8 35.5 1.0
O B:PTR527 2.8 41.3 1.0
O B:HOH736 3.1 62.4 1.0
O B:HOH729 3.2 59.8 1.0
C B:PTR527 3.8 42.7 1.0
C B:GLU524 3.8 36.5 1.0
O B:HOH749 4.0 63.1 1.0
OE2 B:GLU524 4.3 47.5 1.0
N B:PTR527 4.3 33.7 1.0
CA B:PTR527 4.5 35.0 1.0
C B:GLU528 4.5 44.4 1.0
CD B:GLU524 4.5 44.6 1.0
CA B:SER525 4.5 31.0 1.0
N B:SER525 4.6 30.5 1.0
N B:GLU529 4.6 52.8 1.0
CA B:GLU524 4.6 31.8 1.0
N B:GLU528 4.6 45.5 1.0
CB B:GLU529 4.7 66.7 1.0
CG B:GLU524 4.7 37.2 1.0
CA B:GLU528 4.7 41.7 1.0
O B:GLU528 4.8 49.0 1.0
CB B:PTR527 4.8 34.0 1.0
C B:SER525 4.8 36.5 1.0
N B:GLN526 4.9 33.0 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 20:50:24 2024

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