scPDB - 2xwe entry

Protein Data Bank Entry:

PDB ID : 2xwe

Resolution :2.310 Å

Experimental Method : X-ray

Deposition Date : 2010-11-02

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Glucosylceramidase
ID:	GLCM_HUMAN
AC:	P04062
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	3.2.1.45

Chains:

Chain Name:	Percentage of Residues within binding site
A	85 %
B	15 %

Ligand binding site composition:

B-Factor:	16.433
Number of residues:	35
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.332	2305.125

% Hydrophobic	% Polar
45.53	54.47
According to VolSite

Ligand :

HET Code:	AMF
Formula:	C15H29N2O4S
Molecular weight:	333.467 g/mol
DrugBank ID:	DB07370
Buried Surface Area:	60.61 %
Polar Surface area:	123.43 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	5
Rings:	2
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
-35.5896	-16.8421	1.73023

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
O4	OD1	ASP- 127	3.12	132.52	H-Bond (Ligand Donor)	false
O3	OD1	ASP- 127	2.74	149.53	H-Bond (Ligand Donor)	false
C3	CZ2	TRP- 179	4.48	0	Hydrophobic	false
O3	NE1	TRP- 179	2.92	158.53	H-Bond (Protein Donor)	false
O2	ND2	ASN- 234	2.94	164.66	H-Bond (Protein Donor)	false
O1	OE1	GLU- 235	2.62	151.91	H-Bond (Ligand Donor)	false
C15	CD2	LEU- 241	3.82	0	Hydrophobic	false
C2	CZ	PHE- 246	4.09	0	Hydrophobic	false
S1	CE1	TYR- 313	3.6	0	Hydrophobic	false
C1	CE2	TYR- 313	3.92	0	Hydrophobic	false
C9	CD2	TYR- 313	3.73	0	Hydrophobic	false
C11	CB	TYR- 313	4.41	0	Hydrophobic	false
C5	CZ	TYR- 313	3.99	0	Hydrophobic	false
C12	CD2	LEU- 314	3.95	0	Hydrophobic	false
C15	CZ	PHE- 316	4.25	0	Hydrophobic	false
O2	OE1	GLU- 340	2.79	148.51	H-Bond (Ligand Donor)	false
O2	OE2	GLU- 340	3.14	144.28	H-Bond (Ligand Donor)	false
C6	SG	CYS- 342	3.88	0	Hydrophobic	false
S1	CB	SER- 345	3.2	0	Hydrophobic	false
O4	NE1	TRP- 381	2.93	141.78	H-Bond (Protein Donor)	false
C4	CE2	TRP- 381	4.28	0	Hydrophobic	false
C3	CZ2	TRP- 381	3.92	0	Hydrophobic	false
C6	CG1	VAL- 398	3.79	0	Hydrophobic	false
O1	O	HOH- 2132	3.28	131.9	H-Bond (Ligand Donor)	false