Magnesium in PDB 6ckx: Structure of CDK12/Cyck in Complex with A Small Molecule Inhibitor N- (4-(1-Methyl-1H-Pyrazol-4-Yl)Phenyl)-N-((1R,4R)-4-(Quinazolin-2- Ylamino)Cyclohexyl)Acetamide

Enzymatic activity of Structure of CDK12/Cyck in Complex with A Small Molecule Inhibitor N- (4-(1-Methyl-1H-Pyrazol-4-Yl)Phenyl)-N-((1R,4R)-4-(Quinazolin-2- Ylamino)Cyclohexyl)Acetamide

All present enzymatic activity of Structure of CDK12/Cyck in Complex with A Small Molecule Inhibitor N- (4-(1-Methyl-1H-Pyrazol-4-Yl)Phenyl)-N-((1R,4R)-4-(Quinazolin-2- Ylamino)Cyclohexyl)Acetamide:
2.7.11.22; 2.7.11.23;

Protein crystallography data

The structure of Structure of CDK12/Cyck in Complex with A Small Molecule Inhibitor N- (4-(1-Methyl-1H-Pyrazol-4-Yl)Phenyl)-N-((1R,4R)-4-(Quinazolin-2- Ylamino)Cyclohexyl)Acetamide, PDB code: 6ckx was solved by M.G.Klein, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.64 / 2.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 96.596, 107.530, 138.324, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 25.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of CDK12/Cyck in Complex with A Small Molecule Inhibitor N- (4-(1-Methyl-1H-Pyrazol-4-Yl)Phenyl)-N-((1R,4R)-4-(Quinazolin-2- Ylamino)Cyclohexyl)Acetamide (pdb code 6ckx). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Structure of CDK12/Cyck in Complex with A Small Molecule Inhibitor N- (4-(1-Methyl-1H-Pyrazol-4-Yl)Phenyl)-N-((1R,4R)-4-(Quinazolin-2- Ylamino)Cyclohexyl)Acetamide, PDB code: 6ckx:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 6ckx

Go back to Magnesium Binding Sites List in 6ckx
Magnesium binding site 1 out of 3 in the Structure of CDK12/Cyck in Complex with A Small Molecule Inhibitor N- (4-(1-Methyl-1H-Pyrazol-4-Yl)Phenyl)-N-((1R,4R)-4-(Quinazolin-2- Ylamino)Cyclohexyl)Acetamide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of CDK12/Cyck in Complex with A Small Molecule Inhibitor N- (4-(1-Methyl-1H-Pyrazol-4-Yl)Phenyl)-N-((1R,4R)-4-(Quinazolin-2- Ylamino)Cyclohexyl)Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1101

b:86.1
occ:1.00
 O A:HOH1201 2.3 72.0 1.0
OD2 A:ASP877 2.4 76.0 1.0
OD1 A:ASN864 2.5 81.3 1.0
CG A:ASN864 3.3 70.7 1.0
ND2 A:ASN864 3.4 73.1 1.0
CG A:ASP877 3.5 77.1 1.0
CB A:ASP877 4.1 73.9 1.0
CE A:LYS861 4.5 75.7 1.0
OD2 A:ASP859 4.5 82.7 1.0
OG A:SER863 4.5 81.7 1.0
OD1 A:ASP877 4.5 82.0 1.0
NZ A:LYS861 4.5 81.3 1.0
CB A:ASN864 4.8 65.6 1.0

Magnesium binding site 2 out of 3 in 6ckx

Go back to Magnesium Binding Sites List in 6ckx
Magnesium binding site 2 out of 3 in the Structure of CDK12/Cyck in Complex with A Small Molecule Inhibitor N- (4-(1-Methyl-1H-Pyrazol-4-Yl)Phenyl)-N-((1R,4R)-4-(Quinazolin-2- Ylamino)Cyclohexyl)Acetamide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of CDK12/Cyck in Complex with A Small Molecule Inhibitor N- (4-(1-Methyl-1H-Pyrazol-4-Yl)Phenyl)-N-((1R,4R)-4-(Quinazolin-2- Ylamino)Cyclohexyl)Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg301

b:81.7
occ:1.00
 OE2 B:GLU158 2.7 91.5 1.0
OE1 B:GLU107 3.7 82.6 1.0
CD B:GLU158 3.8 94.7 1.0
OD2 B:ASP69 3.9 66.9 1.0
OE2 B:GLU107 4.0 80.0 1.0
O B:VAL157 4.1 71.5 1.0
OE1 B:GLU158 4.2 0.1 1.0
CD B:GLU107 4.3 76.8 1.0
OE1 B:GLN162 4.5 78.5 1.0
CG B:ASP69 4.6 61.0 1.0

Magnesium binding site 3 out of 3 in 6ckx

Go back to Magnesium Binding Sites List in 6ckx
Magnesium binding site 3 out of 3 in the Structure of CDK12/Cyck in Complex with A Small Molecule Inhibitor N- (4-(1-Methyl-1H-Pyrazol-4-Yl)Phenyl)-N-((1R,4R)-4-(Quinazolin-2- Ylamino)Cyclohexyl)Acetamide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of CDK12/Cyck in Complex with A Small Molecule Inhibitor N- (4-(1-Methyl-1H-Pyrazol-4-Yl)Phenyl)-N-((1R,4R)-4-(Quinazolin-2- Ylamino)Cyclohexyl)Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1101

b:76.7
occ:1.00
 OD2 C:ASP877 2.3 80.1 1.0
OD1 C:ASN864 2.3 73.2 1.0
CG C:ASN864 3.3 68.4 1.0
CG C:ASP877 3.4 77.9 1.0
ND2 C:ASN864 3.6 69.1 1.0
CB C:ASP877 3.7 75.7 1.0
OD1 C:ASP877 4.5 78.4 1.0
CB C:ASN864 4.7 65.4 1.0
OG C:SER863 4.7 86.4 1.0
O C:SER863 4.7 76.3 1.0

Reference:

M.Ito, T.Tanaka, A.Toita, N.Uchiyama, H.Kokubo, N.Morishita, M.G.Klein, H.Zou, M.Murakami, M.Kondo, T.Sameshima, S.Araki, S.Endo, T.Kawamoto, G.B.Morin, S.A.Aparicio, A.Nakanishi, H.Maezaki, Y.Imaeda. Discovery of 3-Benzyl-1-( Trans-4-((5-Cyanopyridin-2-Yl)Amino)Cyclohexyl)-1-Arylurea Derivatives As Novel and Selective Cyclin-Dependent Kinase 12 (CDK12) Inhibitors. J. Med. Chem. V. 61 7710 2018.
ISSN: ISSN 1520-4804
PubMed: 30067358
DOI: 10.1021/ACS.JMEDCHEM.8B00683
Page generated: Mon Dec 14 22:31:16 2020

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