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Potassium in PDB 5dsx: Crystal Structure of DOT1L in Complex with Inhibitor CPD10 [6'-Chloro- 1,4-Dimethyl-5'-(2-Methyl-6-((4-(Methylamino)Pyrimidin-2-Yl)Amino)- 1H-Indol-1-Yl)-[3,3'-Bipyridin]-2(1H)-One]

Enzymatic activity of Crystal Structure of DOT1L in Complex with Inhibitor CPD10 [6'-Chloro- 1,4-Dimethyl-5'-(2-Methyl-6-((4-(Methylamino)Pyrimidin-2-Yl)Amino)- 1H-Indol-1-Yl)-[3,3'-Bipyridin]-2(1H)-One]

All present enzymatic activity of Crystal Structure of DOT1L in Complex with Inhibitor CPD10 [6'-Chloro- 1,4-Dimethyl-5'-(2-Methyl-6-((4-(Methylamino)Pyrimidin-2-Yl)Amino)- 1H-Indol-1-Yl)-[3,3'-Bipyridin]-2(1H)-One]:
2.1.1.43;

Protein crystallography data

The structure of Crystal Structure of DOT1L in Complex with Inhibitor CPD10 [6'-Chloro- 1,4-Dimethyl-5'-(2-Methyl-6-((4-(Methylamino)Pyrimidin-2-Yl)Amino)- 1H-Indol-1-Yl)-[3,3'-Bipyridin]-2(1H)-One], PDB code: 5dsx 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) 45.65 / 2.41
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 158.140, 158.140, 73.980, 90.00, 90.00, 120.00
R / Rfree (%) 17.2 / 20.2

Other elements in 5dsx:

The structure of Crystal Structure of DOT1L in Complex with Inhibitor CPD10 [6'-Chloro- 1,4-Dimethyl-5'-(2-Methyl-6-((4-(Methylamino)Pyrimidin-2-Yl)Amino)- 1H-Indol-1-Yl)-[3,3'-Bipyridin]-2(1H)-One] also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of DOT1L in Complex with Inhibitor CPD10 [6'-Chloro- 1,4-Dimethyl-5'-(2-Methyl-6-((4-(Methylamino)Pyrimidin-2-Yl)Amino)- 1H-Indol-1-Yl)-[3,3'-Bipyridin]-2(1H)-One] (pdb code 5dsx). 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 CPD10 [6'-Chloro- 1,4-Dimethyl-5'-(2-Methyl-6-((4-(Methylamino)Pyrimidin-2-Yl)Amino)- 1H-Indol-1-Yl)-[3,3'-Bipyridin]-2(1H)-One], PDB code: 5dsx:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in 5dsx

Go back to Potassium Binding Sites List in 5dsx
Potassium binding site 1 out of 2 in the Crystal Structure of DOT1L in Complex with Inhibitor CPD10 [6'-Chloro- 1,4-Dimethyl-5'-(2-Methyl-6-((4-(Methylamino)Pyrimidin-2-Yl)Amino)- 1H-Indol-1-Yl)-[3,3'-Bipyridin]-2(1H)-One]


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 CPD10 [6'-Chloro- 1,4-Dimethyl-5'-(2-Methyl-6-((4-(Methylamino)Pyrimidin-2-Yl)Amino)- 1H-Indol-1-Yl)-[3,3'-Bipyridin]-2(1H)-One] within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1001

b:0.4
occ:1.00
 OD1 A:ASN57 2.3 0.9 1.0
O A:MET55 2.7 0.7 1.0
O A:LYS52 3.1 0.5 1.0
O A:LEU53 3.1 0.1 1.0
CG A:ASN57 3.6 0.5 1.0
C A:LEU53 3.8 0.1 1.0
C A:MET55 4.0 0.7 1.0
N A:ASN57 4.1 0.5 1.0
CA A:LEU53 4.2 0.9 1.0
C A:LYS52 4.2 0.1 1.0
ND2 A:ASN57 4.4 0.4 1.0
CB A:ASN57 4.6 0.1 1.0
CA A:ASN57 4.6 0.3 1.0
N A:LEU53 4.6 0.4 1.0
N A:MET55 4.8 0.9 1.0
N A:GLU56 4.8 0.4 1.0
CA A:GLU56 4.8 0.5 1.0
C A:GLU56 4.8 0.4 1.0
N A:ALA54 4.8 0.0 1.0
C A:ALA54 4.9 0.7 1.0
CA A:MET55 4.9 0.1 1.0

Potassium binding site 2 out of 2 in 5dsx

Go back to Potassium Binding Sites List in 5dsx
Potassium binding site 2 out of 2 in the Crystal Structure of DOT1L in Complex with Inhibitor CPD10 [6'-Chloro- 1,4-Dimethyl-5'-(2-Methyl-6-((4-(Methylamino)Pyrimidin-2-Yl)Amino)- 1H-Indol-1-Yl)-[3,3'-Bipyridin]-2(1H)-One]


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 CPD10 [6'-Chloro- 1,4-Dimethyl-5'-(2-Methyl-6-((4-(Methylamino)Pyrimidin-2-Yl)Amino)- 1H-Indol-1-Yl)-[3,3'-Bipyridin]-2(1H)-One] within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1001

b:73.1
occ:1.00
 O B:MET55 2.5 56.6 1.0
O B:LYS52 2.5 54.1 1.0
O B:HOH1179 2.9 61.3 1.0
OD1 B:ASN57 2.9 87.1 1.0
O B:HOH1175 2.9 66.7 1.0
O B:LEU53 3.1 54.0 1.0
C B:LEU53 3.5 54.6 1.0
C B:LYS52 3.6 52.8 1.0
C B:MET55 3.7 57.6 1.0
CA B:LEU53 3.7 53.4 1.0
CG B:ASN57 4.1 96.5 1.0
N B:LEU53 4.1 51.2 1.0
N B:MET55 4.3 48.8 1.0
N B:ASN57 4.4 74.7 1.0
N B:ALA54 4.5 49.8 1.0
CA B:MET55 4.5 49.9 1.0
C B:ALA54 4.6 52.0 1.0
O B:HOH1102 4.6 48.0 1.0
N B:GLU56 4.7 59.8 1.0
CA B:GLU56 4.9 62.1 1.0
CA B:LYS52 4.9 46.5 1.0
O B:ALA54 4.9 52.3 1.0
ND2 B:ASN57 5.0 86.5 1.0
CA B:ASN57 5.0 76.4 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 13:17:39 2024

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