scPDB - 2jf6 entry

Protein Data Bank Entry:

PDB ID : 2jf6

Resolution :2.820 Å

Experimental Method : X-ray

Deposition Date : 2007-01-26

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Strictosidine-O-beta-D-glucosidase
ID:	SG1_RAUSE
AC:	Q8GU20
Organism:	Rauvolfia serpentina
Reign:	Eukaryota
TaxID:	4060
EC Number:	3.2.1.105

Chains:

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

Ligand binding site composition:

B-Factor:	7.984
Number of residues:	37
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.742	823.500

% Hydrophobic	% Polar
47.13	52.87
According to VolSite

Ligand :

HET Code:	S55
Formula:	C27H37N2O9
Molecular weight:	533.591 g/mol
DrugBank ID:	-
Buried Surface Area:	65.31 %
Polar Surface area:	167.3 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	6
Rings:	5
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
28.6392	112.24	-26.8876

Binding mode :

What is Poseview ?

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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
O35	NE2	GLN- 57	3.19	163.23	H-Bond (Protein Donor)	false
O36	NE2	HIS- 161	2.83	144.11	H-Bond (Ligand Donor)	false
C29	CH2	TRP- 162	4.09	0	Hydrophobic	false
C26	CH2	TRP- 162	3.64	0	Hydrophobic	false
C26	CG2	THR- 210	3.51	0	Hydrophobic	false
C25	CE2	PHE- 221	4.41	0	Hydrophobic	false
C26	CD2	PHE- 221	4.19	0	Hydrophobic	false
C23	CG	MET- 275	3.71	0	Hydrophobic	false
C23	CE	MET- 297	3.35	0	Hydrophobic	false
C17	CE1	TYR- 345	4.05	0	Hydrophobic	false
C28	CE1	TYR- 345	3.62	0	Hydrophobic	false
C32	CZ	TYR- 345	3.73	0	Hydrophobic	false
C21	CZ2	TRP- 388	3.84	0	Hydrophobic	false
C23	CH2	TRP- 388	3.53	0	Hydrophobic	false
C14	CZ3	TRP- 388	4.26	0	Hydrophobic	false
C10	CB	TRP- 388	3.78	0	Hydrophobic	false
C5	CB	TRP- 388	3.67	0	Hydrophobic	false
O37	OE1	GLU- 416	2.59	138.07	H-Bond (Ligand Donor)	false
O37	OE2	GLU- 416	2.9	147.68	H-Bond (Ligand Donor)	false
C2	CG2	VAL- 420	4.33	0	Hydrophobic	false
C31	CE2	TRP- 465	3.89	0	Hydrophobic	false
O36	NE1	TRP- 473	2.87	153.05	H-Bond (Protein Donor)	false
C3	CD2	LEU- 475	4.02	0	Hydrophobic	false
C2	CD2	LEU- 475	4.01	0	Hydrophobic	false
C33	CZ	TYR- 481	3.46	0	Hydrophobic	false