scPDB - 4f70 entry

Protein Data Bank Entry:

PDB ID : 4f70

Resolution :3.000 Å

Experimental Method : X-ray

Deposition Date : 2012-05-15

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Cyclin-dependent kinase 8
ID:	CDK8_HUMAN
AC:	P49336
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.7.11.22

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	52.477
Number of residues:	30
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.978	435.375

% Hydrophobic	% Polar
55.81	44.19
According to VolSite

Ligand :

HET Code:	0ST
Formula:	C21H32N5O2
Molecular weight:	386.511 g/mol
DrugBank ID:	-
Buried Surface Area:	56.83 %
Polar Surface area:	72.62 Å2

Number of
H-Bond Acceptors:	3
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
39.271	-21.2799	103.094

Binding mode :

What is Poseview ?

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Image generated by PoseView

Protein

Binding Site

Ligand

Interaction pattern

hydrophobic (CA)

aromatic (CZ)

hydrogen bond acceptor (O)

hydrogen bond acceptor/donor (OG)

hydrogen bond donor (N)

positively ionized (NZ)

negatively ionized (OD1)

metal (ZN)

Legend:

Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand

Image generated using PoseView by BioSolveIT

Ligand	Protein		Interaction
Atom	Atom	Residue	Distance (Å)	Angle (°)	Type
C7	CB	SER- 62	3.61	0	Hydrophobic	false
N17	OE2	GLU- 66	3.32	147.9	H-Bond (Ligand Donor)	false
C4	CG	GLU- 66	3.82	0	Hydrophobic	false
C1	CB	GLU- 66	3.42	0	Hydrophobic	false
C15	CD2	LEU- 70	4.09	0	Hydrophobic	false
C15	CD1	LEU- 73	3.81	0	Hydrophobic	false
C15	CG1	VAL- 78	4.48	0	Hydrophobic	false
C14	CG1	VAL- 78	4.06	0	Hydrophobic	false
C15	CD2	LEU- 142	4.14	0	Hydrophobic	false
C14	CD1	LEU- 142	4.37	0	Hydrophobic	false
C14	CG2	ILE- 171	3.96	0	Hydrophobic	false
C27	CB	ALA- 172	3.99	0	Hydrophobic	false
O21	N	ASP- 173	3.27	148.14	H-Bond (Protein Donor)	false
C6	CB	ASP- 173	4.12	0	Hydrophobic	false
C16	CB	ASP- 173	4.01	0	Hydrophobic	false
C27	CB	MET- 174	3.71	0	Hydrophobic	false