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Potassium in PDB 5dry: Crystal Structure of DOT1L in Complex with Inhibitor CPD3 [N-(1-(2- Chlorophenyl)-1H-Indol-6-Yl)-2-(2-(5-(2-Chlorophenyl)-1H-Tetrazol-1- Yl)Acetyl)Hydrazinecarboxamide]

Enzymatic activity of Crystal Structure of DOT1L in Complex with Inhibitor CPD3 [N-(1-(2- Chlorophenyl)-1H-Indol-6-Yl)-2-(2-(5-(2-Chlorophenyl)-1H-Tetrazol-1- Yl)Acetyl)Hydrazinecarboxamide]

All present enzymatic activity of Crystal Structure of DOT1L in Complex with Inhibitor CPD3 [N-(1-(2- Chlorophenyl)-1H-Indol-6-Yl)-2-(2-(5-(2-Chlorophenyl)-1H-Tetrazol-1- Yl)Acetyl)Hydrazinecarboxamide]:
2.1.1.43;

Protein crystallography data

The structure of Crystal Structure of DOT1L in Complex with Inhibitor CPD3 [N-(1-(2- Chlorophenyl)-1H-Indol-6-Yl)-2-(2-(5-(2-Chlorophenyl)-1H-Tetrazol-1- Yl)Acetyl)Hydrazinecarboxamide], PDB code: 5dry was solved by C.Scheufler, C.Gaul, C.Be, H.Moebitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.83 / 2.41
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 158.760, 158.760, 74.460, 90.00, 90.00, 120.00
R / Rfree (%) 17.7 / 19.9

Other elements in 5dry:

The structure of Crystal Structure of DOT1L in Complex with Inhibitor CPD3 [N-(1-(2- Chlorophenyl)-1H-Indol-6-Yl)-2-(2-(5-(2-Chlorophenyl)-1H-Tetrazol-1- Yl)Acetyl)Hydrazinecarboxamide] also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of DOT1L in Complex with Inhibitor CPD3 [N-(1-(2- Chlorophenyl)-1H-Indol-6-Yl)-2-(2-(5-(2-Chlorophenyl)-1H-Tetrazol-1- Yl)Acetyl)Hydrazinecarboxamide] (pdb code 5dry). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 2 binding sites of Potassium where determined in the Crystal Structure of DOT1L in Complex with Inhibitor CPD3 [N-(1-(2- Chlorophenyl)-1H-Indol-6-Yl)-2-(2-(5-(2-Chlorophenyl)-1H-Tetrazol-1- Yl)Acetyl)Hydrazinecarboxamide], PDB code: 5dry:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in 5dry

Go back to Potassium Binding Sites List in 5dry
Potassium binding site 1 out of 2 in the Crystal Structure of DOT1L in Complex with Inhibitor CPD3 [N-(1-(2- Chlorophenyl)-1H-Indol-6-Yl)-2-(2-(5-(2-Chlorophenyl)-1H-Tetrazol-1- Yl)Acetyl)Hydrazinecarboxamide]


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of DOT1L in Complex with Inhibitor CPD3 [N-(1-(2- Chlorophenyl)-1H-Indol-6-Yl)-2-(2-(5-(2-Chlorophenyl)-1H-Tetrazol-1- Yl)Acetyl)Hydrazinecarboxamide] within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K401

b:0.1
occ:1.00
 O A:HOH614 2.5 83.3 1.0
O A:MET55 2.7 96.9 1.0
O A:HOH591 2.8 69.9 1.0
ND2 A:ASN57 3.4 0.3 1.0
O A:LEU53 3.7 96.6 1.0
O A:LYS52 3.8 94.2 1.0
CG A:ASN57 3.9 0.4 1.0
OD1 A:ASN57 4.0 0.0 1.0
C A:MET55 4.0 95.6 1.0
O A:HOH606 4.1 62.7 1.0
N A:ASN57 4.3 94.2 1.0
C A:LEU53 4.4 96.6 1.0
C A:GLU56 4.6 97.1 1.0
CA A:GLU56 4.7 94.8 1.0
CA A:ASN57 4.8 92.8 1.0
CA A:LEU53 4.8 93.8 1.0
N A:GLU56 4.8 93.6 1.0
N A:MET55 4.9 89.0 1.0
CB A:ASN57 4.9 95.7 1.0
C A:LYS52 4.9 93.8 1.0
O A:HOH572 4.9 77.8 1.0
CA A:MET55 5.0 87.9 1.0

Potassium binding site 2 out of 2 in 5dry

Go back to Potassium Binding Sites List in 5dry
Potassium binding site 2 out of 2 in the Crystal Structure of DOT1L in Complex with Inhibitor CPD3 [N-(1-(2- Chlorophenyl)-1H-Indol-6-Yl)-2-(2-(5-(2-Chlorophenyl)-1H-Tetrazol-1- Yl)Acetyl)Hydrazinecarboxamide]


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of DOT1L in Complex with Inhibitor CPD3 [N-(1-(2- Chlorophenyl)-1H-Indol-6-Yl)-2-(2-(5-(2-Chlorophenyl)-1H-Tetrazol-1- Yl)Acetyl)Hydrazinecarboxamide] within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1001

b:67.3
occ:1.00
 O B:LYS52 2.5 50.8 1.0
O B:MET55 2.8 46.0 1.0
O B:LEU53 2.9 50.5 1.0
ND2 B:ASN57 3.2 87.9 1.0
O B:HOH1230 3.3 57.7 1.0
O B:HOH1222 3.3 52.0 1.0
C B:LEU53 3.4 47.5 1.0
O B:HOH1233 3.6 68.1 1.0
CA B:LEU53 3.6 43.6 1.0
C B:LYS52 3.6 48.0 1.0
C B:MET55 4.0 48.0 1.0
N B:LEU53 4.0 42.6 1.0
CG B:ASN57 4.1 96.9 1.0
N B:MET55 4.4 39.5 1.0
N B:ALA54 4.4 39.9 1.0
C B:ALA54 4.6 41.6 1.0
CB B:ASN57 4.6 65.7 1.0
O B:HOH1106 4.6 40.0 1.0
N B:ASN57 4.7 59.6 1.0
CA B:MET55 4.7 41.0 1.0
O B:ALA54 4.9 42.0 1.0
CA B:LYS52 4.9 42.7 1.0
CB B:LEU53 5.0 45.4 1.0
OD1 B:ASN57 5.0 94.3 1.0
N B:GLU56 5.0 50.2 1.0
CA B:ALA54 5.0 38.5 1.0

Reference:

C.Chen, H.Zhu, F.Stauffer, G.Caravatti, S.Vollmer, R.Machauer, P.Holzer, H.Mobitz, C.Scheufler, M.Klumpp, R.Tiedt, K.S.Beyer, K.Calkins, D.Guthy, M.Kiffe, J.Zhang, C.Gaul. Discovery of Novel DOT1L Inhibitors Through A Structure-Based Fragmentation Approach. Acs Med.Chem.Lett. V. 7 735 2016.
ISSN: ISSN 1948-5875
PubMed: 27563395
DOI: 10.1021/ACSMEDCHEMLETT.6B00167
Page generated: Mon Aug 12 13:17:14 2024

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