scPDB - 4f7j entry

Protein Data Bank Entry:

PDB ID : 4f7j

Resolution :2.600 Å

Experimental Method : X-ray

Deposition Date : 2012-05-16

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:	53.566
Number of residues:	29
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.257	280.125

% Hydrophobic	% Polar
61.45	38.55
According to VolSite

Ligand :

HET Code:	0SU
Formula:	C17H24N4O2
Molecular weight:	316.398 g/mol
DrugBank ID:	-
Buried Surface Area:	71.67 %
Polar Surface area:	79.18 Å2

Number of
H-Bond Acceptors:	3
H-Bond Donors:	3
Rings:	2
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
-3.0253	-21.1952	153.04

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
C16	CE1	TYR- 32	4.42	0	Hydrophobic	false
C21	CG2	VAL- 35	4.24	0	Hydrophobic	false
C21	CD	LYS- 52	3.85	0	Hydrophobic	false
O22	NZ	LYS- 52	3.1	132.39	H-Bond (Protein Donor)	false
C16	CB	SER- 62	3.96	0	Hydrophobic	false
C1	CG	ARG- 65	4.1	0	Hydrophobic	false
N19	OE2	GLU- 66	3.18	139.97	H-Bond (Ligand Donor)	false
N17	OE2	GLU- 66	2.96	151.09	H-Bond (Ligand Donor)	false
C1	CB	GLU- 66	3.5	0	Hydrophobic	false
C4	CG	GLU- 66	3.82	0	Hydrophobic	false
C2	CD1	LEU- 70	4.11	0	Hydrophobic	false
C14	CD1	LEU- 73	4	0	Hydrophobic	false
C14	CG1	VAL- 78	3.62	0	Hydrophobic	false
C15	CD1	LEU- 142	4.36	0	Hydrophobic	false
C14	CD2	LEU- 142	4.02	0	Hydrophobic	false
C13	CG1	VAL- 147	4.23	0	Hydrophobic	false
C15	CG2	ILE- 171	3.9	0	Hydrophobic	false
O23	N	ASP- 173	3.19	162.65	H-Bond (Protein Donor)	false
C15	CB	ASP- 173	4.4	0	Hydrophobic	false
C6	CB	ASP- 173	4.02	0	Hydrophobic	false
C21	CE	MET- 174	3.95	0	Hydrophobic	false