scPDB - 2j0d entry

Protein Data Bank Entry:

PDB ID : 2j0d

Resolution :2.750 Å

Experimental Method : X-ray

Deposition Date : 2006-08-02

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Cytochrome P450 3A4
ID:	CP3A4_HUMAN
AC:	P08684
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:	40.020
Number of residues:	30
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.936	1677.375

% Hydrophobic	% Polar
50.10	49.90
According to VolSite

Ligand :

HET Code:	ERY
Formula:	C37H68NO13
Molecular weight:	734.935 g/mol
DrugBank ID:	DB00199
Buried Surface Area:	41.24 %
Polar Surface area:	195.11 Å2

Number of
H-Bond Acceptors:	13
H-Bond Donors:	6
Rings:	3
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
-14.0335	-11.2871	26.6991

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
C8	CZ	PHE- 108	4.44	0	Hydrophobic	false
C32	CE2	PHE- 108	3.52	0	Hydrophobic	false
O11	OG	SER- 119	3.33	147.67	H-Bond (Protein Donor)	false
C26	CE1	PHE- 213	3.87	0	Hydrophobic	false
C33	CZ	PHE- 241	4.45	0	Hydrophobic	false
C34	CD1	ILE- 301	3.84	0	Hydrophobic	false
C34	CB	PHE- 304	3.79	0	Hydrophobic	false
C33	CD1	PHE- 304	3.79	0	Hydrophobic	false
C34	CB	ALA- 305	3.78	0	Hydrophobic	false
C37	CG2	THR- 309	3.98	0	Hydrophobic	false
C37	CB	ALA- 370	3.71	0	Hydrophobic	false
C20	CD	ARG- 372	4.07	0	Hydrophobic	false
C31	CD1	LEU- 482	4.05	0	Hydrophobic	false