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Calcium in PDB 4lue: Crystal Structure of Hck in Complex with 7-[Trans-4-(4- Methylpiperazin-1-Yl)Cyclohexyl]-5-(4-Phenoxyphenyl)-7H-Pyrrolo[2,3- D]Pyrimidin-4-Amine (Resulting From Displacement of SKF86002)

Enzymatic activity of Crystal Structure of Hck in Complex with 7-[Trans-4-(4- Methylpiperazin-1-Yl)Cyclohexyl]-5-(4-Phenoxyphenyl)-7H-Pyrrolo[2,3- D]Pyrimidin-4-Amine (Resulting From Displacement of SKF86002)

All present enzymatic activity of Crystal Structure of Hck in Complex with 7-[Trans-4-(4- Methylpiperazin-1-Yl)Cyclohexyl]-5-(4-Phenoxyphenyl)-7H-Pyrrolo[2,3- D]Pyrimidin-4-Amine (Resulting From Displacement of SKF86002):
2.7.10.2;

Protein crystallography data

The structure of Crystal Structure of Hck in Complex with 7-[Trans-4-(4- Methylpiperazin-1-Yl)Cyclohexyl]-5-(4-Phenoxyphenyl)-7H-Pyrrolo[2,3- D]Pyrimidin-4-Amine (Resulting From Displacement of SKF86002), PDB code: 4lue was solved by L.J.Parker, A.Tanaka, N.Handa, K.Honda, Y.Tomabechi, M.Shirouzu, S.Yokoyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.77 / 3.04
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 73.400, 93.530, 181.490, 90.00, 90.00, 90.00
R / Rfree (%) 20.5 / 25.6

Other elements in 4lue:

The structure of Crystal Structure of Hck in Complex with 7-[Trans-4-(4- Methylpiperazin-1-Yl)Cyclohexyl]-5-(4-Phenoxyphenyl)-7H-Pyrrolo[2,3- D]Pyrimidin-4-Amine (Resulting From Displacement of SKF86002) 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 in Complex with 7-[Trans-4-(4- Methylpiperazin-1-Yl)Cyclohexyl]-5-(4-Phenoxyphenyl)-7H-Pyrrolo[2,3- D]Pyrimidin-4-Amine (Resulting From Displacement of SKF86002) (pdb code 4lue). 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 in Complex with 7-[Trans-4-(4- Methylpiperazin-1-Yl)Cyclohexyl]-5-(4-Phenoxyphenyl)-7H-Pyrrolo[2,3- D]Pyrimidin-4-Amine (Resulting From Displacement of SKF86002), PDB code: 4lue:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 4lue

Go back to Calcium Binding Sites List in 4lue
Calcium binding site 1 out of 2 in the Crystal Structure of Hck in Complex with 7-[Trans-4-(4- Methylpiperazin-1-Yl)Cyclohexyl]-5-(4-Phenoxyphenyl)-7H-Pyrrolo[2,3- D]Pyrimidin-4-Amine (Resulting From Displacement of SKF86002)


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 in Complex with 7-[Trans-4-(4- Methylpiperazin-1-Yl)Cyclohexyl]-5-(4-Phenoxyphenyl)-7H-Pyrrolo[2,3- D]Pyrimidin-4-Amine (Resulting From Displacement of SKF86002) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca601

b:54.8
occ:1.00
 O B:GLU524 2.5 76.3 1.0
O B:PTR527 2.5 87.4 1.0
OE2 A:GLU490 2.6 44.7 1.0
OE1 A:GLU490 2.8 50.3 1.0
CD A:GLU490 3.1 50.4 1.0
C B:PTR527 3.6 64.5 1.0
C B:GLU524 3.7 64.3 1.0
OE2 B:GLU524 3.8 69.5 1.0
O A:HOH709 3.9 60.9 1.0
CD B:GLU524 4.2 76.2 1.0
N B:PTR527 4.3 54.9 1.0
CG B:GLU524 4.4 70.1 1.0
CA B:PTR527 4.4 54.2 1.0
CA B:GLU524 4.5 58.2 1.0
CG A:GLU490 4.6 63.1 1.0
N B:SER525 4.6 51.8 1.0
N B:GLU528 4.6 66.5 1.0
N B:GLU529 4.6 75.8 1.0
CA B:SER525 4.7 49.1 1.0
CB B:GLU529 4.8 81.7 1.0
CA B:GLU528 4.8 65.3 1.0
C B:GLU528 4.8 57.4 1.0
CB B:PTR527 4.8 50.0 1.0
N B:GLN526 4.9 69.0 1.0
N A:GLU489 5.0 43.6 1.0
OE1 B:GLU524 5.0 73.4 1.0

Calcium binding site 2 out of 2 in 4lue

Go back to Calcium Binding Sites List in 4lue
Calcium binding site 2 out of 2 in the Crystal Structure of Hck in Complex with 7-[Trans-4-(4- Methylpiperazin-1-Yl)Cyclohexyl]-5-(4-Phenoxyphenyl)-7H-Pyrrolo[2,3- D]Pyrimidin-4-Amine (Resulting From Displacement of SKF86002)


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 in Complex with 7-[Trans-4-(4- Methylpiperazin-1-Yl)Cyclohexyl]-5-(4-Phenoxyphenyl)-7H-Pyrrolo[2,3- D]Pyrimidin-4-Amine (Resulting From Displacement of SKF86002) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca601

b:66.8
occ:1.00
 O A:PTR527 2.5 78.8 1.0
O A:GLU524 2.6 65.6 1.0
OE2 B:GLU490 2.7 44.4 1.0
OE1 B:GLU490 3.0 65.6 1.0
CD B:GLU490 3.2 52.6 1.0
C A:PTR527 3.7 60.2 1.0
C A:GLU524 3.8 61.1 1.0
OE2 A:GLU524 3.9 70.8 1.0
CD A:GLU524 4.3 78.1 1.0
N A:PTR527 4.4 52.6 1.0
CG A:GLU524 4.5 69.3 1.0
CA A:PTR527 4.6 49.8 1.0
N A:GLU528 4.6 60.0 1.0
N A:GLU529 4.6 75.7 1.0
CA A:GLU528 4.6 65.5 1.0
CA A:GLU524 4.6 57.9 1.0
N A:SER525 4.7 57.6 1.0
CG B:GLU490 4.7 59.2 1.0
CA A:SER525 4.7 52.4 1.0
C A:GLU528 4.9 57.1 1.0
N B:GLU489 4.9 57.2 1.0
CB B:PRO488 4.9 42.1 1.0
CB A:GLU529 4.9 81.4 1.0
CB A:PTR527 4.9 50.5 1.0

Reference:

L.J.Parker, S.Taruya, K.Tsuganezawa, N.Ogawa, J.Mikuni, K.Honda, T.Tomabechi, N.Handa, M.Shirouzu, S.Yokoyama, A.Tanaka. Kinase Crystal Identification and Atp-Competitive Inhibitor Screening Using the Fluorescent Ligand SKF86002 Acta Crystallogr.,Sect.D V. 70 392 2014.
ISSN: ISSN 0907-4449
DOI: 10.1107/S1399004713028654
Page generated: Tue Jul 8 23:59:28 2025

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