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Chlorine 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:

Calcium (Ca) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 2 binding sites of Chlorine 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 Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 3vrz

Go back to Chlorine Binding Sites List in 3vrz
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl602

b:71.7
occ:1.00
 NH2 A:ARG85 2.9 54.5 1.0
NH1 A:ARG123 3.4 41.8 1.0
NH2 A:ARG128 3.4 40.0 1.0
NH1 A:ARG85 3.5 56.4 1.0
NH1 A:ARG128 3.5 49.4 1.0
CZ A:ARG85 3.6 61.4 1.0
CD2 A:LEU125 3.9 39.0 1.0
CZ A:ARG128 3.9 42.4 1.0
CG2 A:VAL111 4.1 48.6 1.0
CD A:ARG123 4.2 44.6 1.0
CZ A:ARG123 4.4 47.0 1.0
NE A:ARG123 4.8 44.9 1.0
NE A:ARG85 4.9 56.1 1.0

Chlorine binding site 2 out of 2 in 3vrz

Go back to Chlorine Binding Sites List in 3vrz
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl602

b:70.8
occ:1.00
 NH2 B:ARG85 2.8 56.7 1.0
NH1 B:ARG123 3.0 44.1 1.0
O B:HOH731 3.3 63.1 1.0
NH2 B:ARG128 3.5 33.4 1.0
NH1 B:ARG128 3.6 42.1 1.0
CZ B:ARG85 3.8 61.5 1.0
NH1 B:ARG85 3.9 57.5 1.0
CZ B:ARG128 3.9 38.8 1.0
CG2 B:VAL111 4.0 47.8 1.0
CZ B:ARG123 4.1 38.1 1.0
CD B:ARG123 4.2 37.5 1.0
CD2 B:LEU125 4.3 43.9 1.0
NE B:ARG123 4.6 36.6 1.0
CB B:VAL111 5.0 47.5 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: Sun Jul 21 07:09:25 2024

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