scPDB - 2vn0 entry

Protein Data Bank Entry:

PDB ID : 2vn0

Resolution :2.700 Å

Experimental Method : X-ray

Deposition Date : 2008-01-30

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Cytochrome P450 2C8
ID:	CP2C8_HUMAN
AC:	P10632
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	56.772
Number of residues:	36
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.992	1684.125

% Hydrophobic	% Polar
58.32	41.68
According to VolSite

Ligand :

HET Code:	TDZ
Formula:	C24H26NO5S
Molecular weight:	440.532 g/mol
DrugBank ID:	DB08607
Buried Surface Area:	62.1 %
Polar Surface area:	112.23 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	1
Rings:	4
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
48.2395	10.7783	-26.6858

Binding mode :

What is Poseview ?

2D View
3D View

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
CAI	CD1	ILE- 106	4.42	0	Hydrophobic	false
CBD	CG2	ILE- 106	3.55	0	Hydrophobic	false
SAS	CD1	ILE- 106	4.36	0	Hydrophobic	false
CAO	CG2	THR- 107	4.24	0	Hydrophobic	false
CAA	CB	PHE- 201	4.22	0	Hydrophobic	false
CAB	CB	ASN- 204	4.14	0	Hydrophobic	false
OAE	ND2	ASN- 204	3.01	136	H-Bond (Protein Donor)	false
CAL	CE2	PHE- 205	4.3	0	Hydrophobic	false
CAC	CE2	PHE- 205	4.11	0	Hydrophobic	false
CAD	CD2	PHE- 205	4.11	0	Hydrophobic	false
CAX	CB	PHE- 205	3.64	0	Hydrophobic	false
CAB	CD1	LEU- 208	3.65	0	Hydrophobic	false
SAS	CD1	LEU- 208	3.63	0	Hydrophobic	false
CAK	CD1	LEU- 208	3.66	0	Hydrophobic	false
CAN	CB	LEU- 208	3.84	0	Hydrophobic	false
CAD	CB	ASN- 209	3.73	0	Hydrophobic	false
OAF	NH2	ARG- 241	2.6	147.27	H-Bond (Protein Donor)	false
CAA	CG2	VAL- 296	4.25	0	Hydrophobic	false
SAS	CG2	VAL- 296	4.07	0	Hydrophobic	false
CAH	CG1	VAL- 296	3.46	0	Hydrophobic	false
CAO	CG2	VAL- 296	3.86	0	Hydrophobic	false
CBA	CG1	VAL- 296	3.99	0	Hydrophobic	false
CBA	CB	GLU- 300	3.98	0	Hydrophobic	false
CAC	CG2	THR- 301	3.88	0	Hydrophobic	false
CAD	CG2	ILE- 476	3.79	0	Hydrophobic	false
CAL	CG2	VAL- 477	4.04	0	Hydrophobic	false