scPDB - 3u57 entry

Protein Data Bank Entry:

PDB ID : 3u57

Resolution :2.430 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:	29.998
Number of residues:	33
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.916	860.625

% Hydrophobic	% Polar
47.45	52.55
According to VolSite

Ligand :

HET Code:	DH8
Formula:	C27H35N2O8
Molecular weight:	515.575 g/mol
DrugBank ID:	-
Buried Surface Area:	56.12 %
Polar Surface area:	142.15 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	6
Rings:	7
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
35.6094	43.0787	38.439

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
O3	OE1	GLN- 36	3.23	128.35	H-Bond (Ligand Donor)	false
O4	NE2	GLN- 36	3.23	175.33	H-Bond (Protein Donor)	false
C2	CH2	TRP- 141	4.36	0	Hydrophobic	false
CBC	CZ3	TRP- 188	4.47	0	Hydrophobic	false
CAN	CG2	THR- 189	3.55	0	Hydrophobic	false
OAC	NE2	HIS- 193	3.28	143.22	H-Bond (Protein Donor)	false
CAI	CD1	LEU- 199	3.73	0	Hydrophobic	false
CAV	CZ	TYR- 200	4.21	0	Hydrophobic	false
CAA	CB	ALA- 274	4.05	0	Hydrophobic	false
C1	CE2	TYR- 347	4.11	0	Hydrophobic	false
CAO	CE2	TRP- 392	3.26	0	Hydrophobic	false
CBI	CZ3	TRP- 392	4.17	0	Hydrophobic	false
O2	OE1	GLU- 420	3.17	161.86	H-Bond (Ligand Donor)	false
C3	CZ2	TRP- 469	3.9	0	Hydrophobic	false
C4	CE2	TRP- 469	4.33	0	Hydrophobic	false
O4	NE1	TRP- 469	2.84	148.67	H-Bond (Protein Donor)	false
O4	OE2	GLU- 476	3.36	139.45	H-Bond (Ligand Donor)	false
O4	OE1	GLU- 476	2.66	142.64	H-Bond (Ligand Donor)	false
O6	OE1	GLU- 476	2.67	134.58	H-Bond (Ligand Donor)	false
O3	NE1	TRP- 477	3.36	172.5	H-Bond (Protein Donor)	false
C6	CE2	PHE- 485	3.49	0	Hydrophobic	false