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Calcium in PDB 3vs0: Crystal Structure of Hck Complexed with A Pyrrolo-Pyrimidine Inhibitor N-[4-(4-Amino-7-Cyclopentyl-7H-Pyrrolo[2,3-D]Pyrimidin-5-Yl) Phenyl]Benzamide

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

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

Protein crystallography data

The structure of Crystal Structure of Hck Complexed with A Pyrrolo-Pyrimidine Inhibitor N-[4-(4-Amino-7-Cyclopentyl-7H-Pyrrolo[2,3-D]Pyrimidin-5-Yl) Phenyl]Benzamide, PDB code: 3vs0 was solved by M.Kuratani, K.Honda, 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) 39.29 / 2.93
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 73.720, 96.050, 181.650, 90.00, 90.00, 90.00
R / Rfree (%) 23.7 / 29.5

Other elements in 3vs0:

The structure of Crystal Structure of Hck Complexed with A Pyrrolo-Pyrimidine Inhibitor N-[4-(4-Amino-7-Cyclopentyl-7H-Pyrrolo[2,3-D]Pyrimidin-5-Yl) Phenyl]Benzamide 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 N-[4-(4-Amino-7-Cyclopentyl-7H-Pyrrolo[2,3-D]Pyrimidin-5-Yl) Phenyl]Benzamide (pdb code 3vs0). 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 N-[4-(4-Amino-7-Cyclopentyl-7H-Pyrrolo[2,3-D]Pyrimidin-5-Yl) Phenyl]Benzamide, PDB code: 3vs0:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 3vs0

Go back to Calcium Binding Sites List in 3vs0
Calcium binding site 1 out of 2 in the Crystal Structure of Hck Complexed with A Pyrrolo-Pyrimidine Inhibitor N-[4-(4-Amino-7-Cyclopentyl-7H-Pyrrolo[2,3-D]Pyrimidin-5-Yl) Phenyl]Benzamide


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

b:82.5
occ:1.00
 O A:GLU524 3.1 55.8 1.0
O A:PTR527 3.1 68.9 1.0
OE1 B:GLU489 3.2 82.5 1.0
OE2 B:GLU490 3.2 64.4 1.0
OE2 A:GLU524 3.3 71.6 1.0
OE1 B:GLU490 3.4 67.2 1.0
CG A:GLU529 3.5 89.7 1.0
CD B:GLU490 3.7 63.2 1.0
CD A:GLU524 3.8 73.9 1.0
CD A:GLU529 3.9 0.9 1.0
N A:GLU529 3.9 95.0 1.0
CB A:GLU529 4.1 94.5 1.0
C A:PTR527 4.2 67.5 1.0
CD B:GLU489 4.2 95.5 1.0
C A:GLU524 4.3 59.4 1.0
CG A:GLU524 4.3 67.8 1.0
OE2 A:GLU529 4.3 97.7 1.0
C A:GLU528 4.4 84.2 1.0
OE1 A:GLU529 4.4 1.0 1.0
OE2 B:GLU489 4.5 95.5 1.0
CA A:GLU529 4.5 0.6 1.0
OE1 A:GLU524 4.5 76.6 1.0
CA A:GLU528 4.6 78.7 1.0
N A:GLU528 4.8 76.7 1.0

Calcium binding site 2 out of 2 in 3vs0

Go back to Calcium Binding Sites List in 3vs0
Calcium binding site 2 out of 2 in the Crystal Structure of Hck Complexed with A Pyrrolo-Pyrimidine Inhibitor N-[4-(4-Amino-7-Cyclopentyl-7H-Pyrrolo[2,3-D]Pyrimidin-5-Yl) Phenyl]Benzamide


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

b:70.3
occ:1.00
 O B:GLU524 3.1 57.3 1.0
OE1 A:GLU489 3.1 84.9 1.0
O B:PTR527 3.2 62.9 1.0
OE1 A:GLU490 3.3 67.1 1.0
OE2 A:GLU490 3.4 59.5 1.0
OE2 A:GLU489 3.7 80.7 1.0
CD A:GLU490 3.7 61.4 1.0
CD A:GLU489 3.8 91.2 1.0
CG B:GLU524 4.0 62.1 1.0
OE2 B:GLU524 4.1 75.8 1.0
CG B:GLU529 4.1 95.7 1.0
CB B:GLU529 4.1 94.4 1.0
CD B:GLU529 4.1 95.0 1.0
N B:GLU529 4.1 81.1 1.0
C B:GLU524 4.2 64.9 1.0
CD B:GLU524 4.3 76.2 1.0
C B:PTR527 4.3 62.2 1.0
OE1 B:GLU529 4.4 99.9 1.0
OE2 B:GLU529 4.5 92.0 1.0
CA B:GLU529 4.7 90.4 1.0
C B:GLU528 4.7 74.9 1.0
CA B:GLU524 4.9 62.1 1.0
CA B:GLU528 4.9 74.8 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 20:50:34 2024

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