scPDB - 4f7n entry

Protein Data Bank Entry:

PDB ID : 4f7n

Resolution :2.650 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:	54.002
Number of residues:	34
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.433	391.500

% Hydrophobic	% Polar
49.14	50.86
According to VolSite

Ligand :

HET Code:	0SV
Formula:	C20H30N4O2
Molecular weight:	358.478 g/mol
DrugBank ID:	-
Buried Surface Area:	69.74 %
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:	8

Mass center Coordinates

X	Y	Z
-3.44638	-21.997	155.409

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
C25	CB	ALA- 50	3.53	0	Hydrophobic	false
C16	CB	SER- 62	3.75	0	Hydrophobic	false
C8	CG	ARG- 65	4.24	0	Hydrophobic	false
N19	OE2	GLU- 66	3.46	145.93	H-Bond (Ligand Donor)	false
N17	OE2	GLU- 66	3.33	156.52	H-Bond (Ligand Donor)	false
C6	CG	GLU- 66	4.06	0	Hydrophobic	false
C7	CB	GLU- 66	3.92	0	Hydrophobic	false
C8	CB	GLU- 66	3.57	0	Hydrophobic	false
C15	CD2	LEU- 70	3.78	0	Hydrophobic	false
C15	CD1	LEU- 73	3.54	0	Hydrophobic	false
C15	CG1	VAL- 78	3.96	0	Hydrophobic	false
C22	CG1	ILE- 79	4.08	0	Hydrophobic	false
C24	CG1	ILE- 79	3.77	0	Hydrophobic	false
C24	CB	PHE- 97	4	0	Hydrophobic	false
C22	CD2	PHE- 97	3.72	0	Hydrophobic	false
O26	O	ASP- 98	2.86	156.42	H-Bond (Ligand Donor)	false
O26	N	ALA- 100	3.2	157.69	H-Bond (Protein Donor)	false
C15	CD2	LEU- 142	4.26	0	Hydrophobic	false
C14	CD1	LEU- 142	4.42	0	Hydrophobic	false
C13	CD1	LEU- 142	4.42	0	Hydrophobic	false
C13	CG1	VAL- 147	4.29	0	Hydrophobic	false
C25	CD1	LEU- 158	3.86	0	Hydrophobic	false
C14	CG2	ILE- 171	3.81	0	Hydrophobic	false
O20	N	ASP- 173	3.17	168.58	H-Bond (Protein Donor)	false
C11	CB	ASP- 173	3.81	0	Hydrophobic	false
C23	SD	MET- 174	4.38	0	Hydrophobic	false