scPDB - 2oyl entry

Protein Data Bank Entry:

PDB ID : 2oyl

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2007-02-22

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Endoglycoceramidase II
ID:	O33853_RHOSO
AC:	O33853
Organism:	Rhodococcus sp
Reign:	Bacteria
TaxID:	1831
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	14.047
Number of residues:	26
Including
Standard Amino Acids:	25
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.244	600.750

% Hydrophobic	% Polar
51.69	48.31
According to VolSite

Ligand :

HET Code:	IDC
Formula:	C14H22N2O9
Molecular weight:	362.332 g/mol
DrugBank ID:	DB02017
Buried Surface Area:	58.24 %
Polar Surface area:	177.89 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	7
Rings:	3
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
27.4837	58.6525	-27.0878

Binding mode :

What is Poseview ?

2D View
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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
C2A	CB	SER- 63	4.49	0	Hydrophobic	false
O6A	NZ	LYS- 66	2.91	162.22	H-Bond (Protein Donor)	false
O3B	NZ	LYS- 66	2.89	155.31	H-Bond (Protein Donor)	false
O3B	NE2	HIS- 135	3.05	151.92	H-Bond (Protein Donor)	false
C6A	CB	ASP- 137	3.96	0	Hydrophobic	false
O3B	OD2	ASP- 137	2.68	171.14	H-Bond (Ligand Donor)	false
C1A	CZ2	TRP- 178	4.27	0	Hydrophobic	false
C5A	CE2	TRP- 178	3.7	0	Hydrophobic	false
C6A	CD2	TRP- 178	3.81	0	Hydrophobic	false
C2B	CH2	TRP- 178	4.25	0	Hydrophobic	false
C4B	CZ2	TRP- 178	3.99	0	Hydrophobic	false
O2B	ND2	ASN- 232	3.11	159.31	H-Bond (Protein Donor)	false
DuAr	DuAr	TYR- 306	3.9	0	Aromatic Face/Face	false
O2B	OE1	GLU- 351	3.1	147.42	H-Bond (Ligand Donor)	false
O2B	OE2	GLU- 351	2.6	145.28	H-Bond (Ligand Donor)	false
O2A	NE1	TRP- 382	3.46	154.55	H-Bond (Protein Donor)	false
C1A	CZ2	TRP- 382	4.05	0	Hydrophobic	false
C3B	CZ2	TRP- 382	3.65	0	Hydrophobic	false
C5B	CE2	TRP- 382	3.68	0	Hydrophobic	false
C6B	CH2	TRP- 389	4.2	0	Hydrophobic	false