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Sodium in PDB 4f6u: Crystal Structure of Human CDK8/Cycc in Complex with Compound 5 (1-[3- Tert-Butyl-1-(4-Methylphenyl)-1H-Pyrazol-5-Yl]-3-[3-(Morpholin-4-Yl) Propyl]Urea)

Enzymatic activity of Crystal Structure of Human CDK8/Cycc in Complex with Compound 5 (1-[3- Tert-Butyl-1-(4-Methylphenyl)-1H-Pyrazol-5-Yl]-3-[3-(Morpholin-4-Yl) Propyl]Urea)

All present enzymatic activity of Crystal Structure of Human CDK8/Cycc in Complex with Compound 5 (1-[3- Tert-Butyl-1-(4-Methylphenyl)-1H-Pyrazol-5-Yl]-3-[3-(Morpholin-4-Yl) Propyl]Urea):
2.7.11.22; 2.7.11.23;

Protein crystallography data

The structure of Crystal Structure of Human CDK8/Cycc in Complex with Compound 5 (1-[3- Tert-Butyl-1-(4-Methylphenyl)-1H-Pyrazol-5-Yl]-3-[3-(Morpholin-4-Yl) Propyl]Urea), PDB code: 4f6u was solved by E.V.Schneider, J.Boettcher, R.Huber, K.Maskos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 85.61 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 71.397, 71.024, 171.217, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 19.8

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Human CDK8/Cycc in Complex with Compound 5 (1-[3- Tert-Butyl-1-(4-Methylphenyl)-1H-Pyrazol-5-Yl]-3-[3-(Morpholin-4-Yl) Propyl]Urea) (pdb code 4f6u). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Human CDK8/Cycc in Complex with Compound 5 (1-[3- Tert-Butyl-1-(4-Methylphenyl)-1H-Pyrazol-5-Yl]-3-[3-(Morpholin-4-Yl) Propyl]Urea), PDB code: 4f6u:

Sodium binding site 1 out of 1 in 4f6u

Go back to Sodium Binding Sites List in 4f6u
Sodium binding site 1 out of 1 in the Crystal Structure of Human CDK8/Cycc in Complex with Compound 5 (1-[3- Tert-Butyl-1-(4-Methylphenyl)-1H-Pyrazol-5-Yl]-3-[3-(Morpholin-4-Yl) Propyl]Urea)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Human CDK8/Cycc in Complex with Compound 5 (1-[3- Tert-Butyl-1-(4-Methylphenyl)-1H-Pyrazol-5-Yl]-3-[3-(Morpholin-4-Yl) Propyl]Urea) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na502

b:58.3
occ:1.00
 ND1 A:HIS140 2.5 52.9 1.0
OD1 A:ASP137 2.6 36.8 1.0
O A:HOH765 2.7 37.0 1.0
O A:ASP137 3.1 29.0 1.0
CE1 A:HIS140 3.3 58.8 1.0
CG A:HIS140 3.5 44.8 1.0
NE2 A:HIS75 3.6 35.4 1.0
N A:TYR141 3.8 28.8 1.0
CG A:ASP137 3.8 36.8 1.0
CB A:HIS140 3.9 33.0 1.0
C A:ASP137 3.9 31.1 1.0
CB A:TYR141 4.1 31.9 1.0
CA A:ASP137 4.2 30.4 1.0
CA A:TYR141 4.2 31.3 1.0
CD2 A:HIS75 4.3 38.0 1.0
C A:HIS140 4.4 31.0 1.0
NE2 A:HIS140 4.5 55.9 1.0
CE1 A:HIS75 4.5 36.3 1.0
CE A:MET330 4.6 39.0 1.0
CD2 A:HIS140 4.6 57.4 1.0
CB A:ASP137 4.6 30.8 1.0
SD A:MET330 4.7 39.9 1.0
CA A:HIS140 4.7 31.9 1.0
OD2 A:ASP137 4.7 32.6 1.0

Reference:

E.V.Schneider, J.Bottcher, R.Huber, K.Maskos, L.Neumann. Structure-Kinetic Relationship Study of CDK8/Cycc Specific Compounds. Proc.Natl.Acad.Sci.Usa V. 110 8081 2013.
ISSN: ISSN 0027-8424
PubMed: 23630251
DOI: 10.1073/PNAS.1305378110
Page generated: Mon Oct 7 15:18:09 2024

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