scPDB - 3zj6 entry

Protein Data Bank Entry:

PDB ID : 3zj6

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 2013-01-17

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Raucaffricine-O-beta-D-glucosidase
ID:	RG1_RAUSE
AC:	Q9SPP9
Organism:	Rauvolfia serpentina
Reign:	Eukaryota
TaxID:	4060
EC Number:	3.2.1.125

Chains:

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

Ligand binding site composition:

B-Factor:	39.617
Number of residues:	29
Including
Standard Amino Acids:	25
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.384	472.500

% Hydrophobic	% Polar
44.29	55.71
According to VolSite

Ligand :

HET Code:	VM2
Formula:	C13H26NO4
Molecular weight:	260.350 g/mol
DrugBank ID:	-
Buried Surface Area:	71.06 %
Polar Surface area:	97.53 Å2

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

Mass center Coordinates

X	Y	Z
-18.0333	35.521	19.5267

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
O3B	OE1	GLN- 36	2.6	138.81	H-Bond (Ligand Donor)	false
O4B	NE2	GLN- 36	2.97	165.02	H-Bond (Protein Donor)	false
O3B	NE2	HIS- 140	2.8	144.33	H-Bond (Protein Donor)	false
C2B	CH2	TRP- 141	3.82	0	Hydrophobic	false
O2B	ND2	ASN- 185	3.14	157.09	H-Bond (Protein Donor)	false
N2B	OE2	GLU- 186	3.33	0	Ionic (Ligand Cationic)	false
N2B	OE1	GLU- 186	2.92	0	Ionic (Ligand Cationic)	false
N2B	OE1	GLU- 186	2.92	165.91	H-Bond (Ligand Donor)	false
C3	CZ3	TRP- 188	4.03	0	Hydrophobic	false
C2	CG2	THR- 189	3.46	0	Hydrophobic	false
C6	CD1	TYR- 347	4.49	0	Hydrophobic	false
C6B	CZ	TYR- 347	3.82	0	Hydrophobic	false
C5	CZ3	TRP- 392	3.5	0	Hydrophobic	false
C6	CH2	TRP- 392	3.49	0	Hydrophobic	false
O2B	OE2	GLU- 420	2.61	128.92	H-Bond (Ligand Donor)	false
O2B	OE1	GLU- 420	2.77	151.81	H-Bond (Ligand Donor)	false
C5B	CE2	TRP- 469	4.21	0	Hydrophobic	false
C3B	CZ2	TRP- 469	3.7	0	Hydrophobic	false
O4B	OE1	GLU- 476	2.69	144.68	H-Bond (Ligand Donor)	false
O6B	OE2	GLU- 476	2.65	146.21	H-Bond (Ligand Donor)	false
O3B	NE1	TRP- 477	2.87	158.61	H-Bond (Protein Donor)	false
C6B	CZ	PHE- 485	4.25	0	Hydrophobic	false
O4B	O	HOH- 2013	3.48	123.05	H-Bond (Protein Donor)	false