scPDB - 3u5y entry

Protein Data Bank Entry:

PDB ID : 3u5y

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2011-10-11

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
A	100 %

Ligand binding site composition:

B-Factor:	35.575
Number of residues:	31
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.792	745.875

% Hydrophobic	% Polar
46.61	53.39
According to VolSite

Ligand :

HET Code:	SCG
Formula:	C17H24O10
Molecular weight:	388.366 g/mol
DrugBank ID:	-
Buried Surface Area:	61.91 %
Polar Surface area:	151.97 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	4
Rings:	2
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
34.5266	43.4571	37.1499

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
O25	NE2	GLN- 36	3.16	176.85	H-Bond (Protein Donor)	false
O26	OE1	GLN- 36	3	138.91	H-Bond (Ligand Donor)	false
O26	NE2	HIS- 140	3.44	146	H-Bond (Protein Donor)	false
C18	CH2	TRP- 141	4.13	0	Hydrophobic	false
O11	NE2	GLN- 186	3.25	157.88	H-Bond (Protein Donor)	false
C6	CG2	THR- 189	3.9	0	Hydrophobic	false
C15	CB	GLN- 276	3.74	0	Hydrophobic	false
C17	CE2	TYR- 347	4.38	0	Hydrophobic	false
C9	CH2	TRP- 392	3.99	0	Hydrophobic	false
O27	OE1	GLU- 420	2.92	143.43	H-Bond (Ligand Donor)	false
O25	NE1	TRP- 469	2.91	135.37	H-Bond (Protein Donor)	false
C19	CZ2	TRP- 469	3.67	0	Hydrophobic	false
O25	OE2	GLU- 476	3.27	134.57	H-Bond (Ligand Donor)	false
O25	OE1	GLU- 476	2.59	148.06	H-Bond (Ligand Donor)	false
O26	NE1	TRP- 477	3	175.48	H-Bond (Protein Donor)	false
C23	CE2	PHE- 485	3.38	0	Hydrophobic	false