scPDB - 2oym entry

Protein Data Bank Entry:

PDB ID : 2oym

Resolution :1.860 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
B	100 %

Ligand binding site composition:

B-Factor:	19.362
Number of residues:	32
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.001	570.375

% Hydrophobic	% Polar
47.34	52.66
According to VolSite

Ligand :

HET Code:	MNI
Formula:	C15H24N3O4
Molecular weight:	310.369 g/mol
DrugBank ID:	-
Buried Surface Area:	61.69 %
Polar Surface area:	109.64 Å2

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

Mass center Coordinates

X	Y	Z
6.51132	50.0696	39.1005

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
O4A	NZ	LYS- 66	3.39	123.57	H-Bond (Protein Donor)	false
C3A	CZ2	TRP- 178	3.88	0	Hydrophobic	false
C7B	CG	GLU- 179	3.52	0	Hydrophobic	false
C8B	CD2	TYR- 182	3.53	0	Hydrophobic	false
C9B	CD2	TYR- 182	3.57	0	Hydrophobic	false
O6A	ND2	ASN- 232	2.84	143.62	H-Bond (Protein Donor)	false
N1B	OE2	GLU- 233	3.45	126.12	H-Bond (Ligand Donor)	false
N1B	OE1	GLU- 233	2.92	152.51	H-Bond (Ligand Donor)	false
N5A	OE2	GLU- 233	3.15	120.05	H-Bond (Ligand Donor)	false
N5A	OE1	GLU- 233	3.01	168.84	H-Bond (Ligand Donor)	false
N5A	OE2	GLU- 233	3.15	0	Ionic (Ligand Cationic)	false
N5A	OE1	GLU- 233	3.01	0	Ionic (Ligand Cationic)	false
C8B	CE1	PHE- 235	3.34	0	Hydrophobic	false
C3B	CB	ALA- 275	4.45	0	Hydrophobic	false
C8B	CB	ILE- 276	3.73	0	Hydrophobic	false
C9B	CD1	ILE- 276	4.17	0	Hydrophobic	false
C5B	CD1	ILE- 276	4.04	0	Hydrophobic	false
N5A	OE2	GLU- 351	3.93	0	Ionic (Ligand Cationic)	false
N5A	OE1	GLU- 351	2.98	0	Ionic (Ligand Cationic)	false
N5A	OE1	GLU- 351	2.98	160.73	H-Bond (Ligand Donor)	false
C6A	CH2	TRP- 382	3.66	0	Hydrophobic	false
C4A	CZ2	TRP- 382	4.12	0	Hydrophobic	false