scPDB - 3rgf entry

Protein Data Bank Entry:

PDB ID : 3rgf

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2011-04-08

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	6.510	6.510	6.510	0.000	6.510	3

List of CHEMBLId :

CHEMBL1336

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:	43.019
Number of residues:	38
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.565	445.500

% Hydrophobic	% Polar
57.58	42.42
According to VolSite

Ligand :

HET Code:	BAX
Formula:	C21H16ClF3N4O3
Molecular weight:	464.825 g/mol
DrugBank ID:	DB00398
Buried Surface Area:	72.74 %
Polar Surface area:	92.35 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	3
Rings:	3
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
-4.96519	2.82772	27.584

Binding mode :

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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
C18	CG2	VAL- 35	4.05	0	Hydrophobic	false
C23	CG1	VAL- 35	4.19	0	Hydrophobic	false
C24	CB	ALA- 50	3.34	0	Hydrophobic	false
C17	CD	LYS- 52	3.56	0	Hydrophobic	false
C3	CG	GLU- 66	3.82	0	Hydrophobic	false
N12	OE2	GLU- 66	2.76	147.35	H-Bond (Ligand Donor)	false
N14	OE2	GLU- 66	2.91	140.04	H-Bond (Ligand Donor)	false
CL11	CD1	LEU- 69	4.28	0	Hydrophobic	false
C3	CG	LEU- 70	4.45	0	Hydrophobic	false
C1	CD2	LEU- 70	3.77	0	Hydrophobic	false
F9	CD1	LEU- 73	3.61	0	Hydrophobic	false
F8	CG1	VAL- 78	3.46	0	Hydrophobic	false
C24	CD1	ILE- 79	3.86	0	Hydrophobic	false
C20	CD1	ILE- 79	3.51	0	Hydrophobic	false
C24	CB	PHE- 97	4.27	0	Hydrophobic	false
N30	O	ALA- 100	2.65	134.1	H-Bond (Ligand Donor)	false
N26	N	ALA- 100	3.26	165.55	H-Bond (Protein Donor)	false
F9	CD2	LEU- 142	3.39	0	Hydrophobic	false
F10	CD1	LEU- 142	3.71	0	Hydrophobic	false
CL11	CG1	VAL- 147	3.56	0	Hydrophobic	false
C20	CD1	LEU- 158	4.48	0	Hydrophobic	false
C28	CD1	LEU- 158	4.15	0	Hydrophobic	false
F8	CG2	ILE- 171	4.16	0	Hydrophobic	false
F10	CG2	ILE- 171	4.15	0	Hydrophobic	false
C21	CB	ALA- 172	3.85	0	Hydrophobic	false
F10	CB	ASP- 173	4.17	0	Hydrophobic	false
C1	CB	ASP- 173	3.62	0	Hydrophobic	false
O15	N	ASP- 173	2.72	177.09	H-Bond (Protein Donor)	false
C21	CG	MET- 174	4.13	0	Hydrophobic	false
C18	CG	MET- 174	4.24	0	Hydrophobic	false
C19	SD	MET- 174	3.73	0	Hydrophobic	false
C28	SD	MET- 174	3.72	0	Hydrophobic	false
C3	CB	PHE- 176	4.26	0	Hydrophobic	false