scPDB - 3lpf entry

Protein Data Bank Entry:

PDB ID : 3lpf

Resolution :2.260 Å

Experimental Method : X-ray

Deposition Date : 2010-02-05

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Beta-glucuronidase
ID:	BGLR_ECOLI
AC:	P05804
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	3.2.1.31

Chains:

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

Ligand binding site composition:

B-Factor:	43.547
Number of residues:	30
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.282	1127.250

% Hydrophobic	% Polar
41.92	58.08
According to VolSite

Ligand :

HET Code:	Z77
Formula:	C22H25N3O3S
Molecular weight:	411.517 g/mol
DrugBank ID:	-
Buried Surface Area:	52.57 %
Polar Surface area:	105.92 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
-25.6128	6.01528	-5.51328

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
CAA	CB	ASP- 163	4.48	0	Hydrophobic	false
CAN	CD2	LEU- 361	3.71	0	Hydrophobic	false
CBB	CD2	LEU- 361	4.16	0	Hydrophobic	false
CAG	CB	ILE- 363	3.6	0	Hydrophobic	false
OAE	OE1	GLU- 413	3.27	155.43	H-Bond (Ligand Donor)	false
OAE	OE2	GLU- 413	3.26	124.71	H-Bond (Ligand Donor)	false
CAK	SD	MET- 447	4.17	0	Hydrophobic	false
CAB	CG	MET- 447	3.9	0	Hydrophobic	false
CAB	CB	PHE- 448	4.05	0	Hydrophobic	false
CAC	CB	PHE- 448	3.71	0	Hydrophobic	false
CAP	CZ	TYR- 472	3.34	0	Hydrophobic	false
CAK	CB	TYR- 472	4.06	0	Hydrophobic	false
CAO	CE1	TYR- 472	3.95	0	Hydrophobic	false
CAB	CG2	VAL- 473	3.82	0	Hydrophobic	false
CAA	CB	THR- 556	4.21	0	Hydrophobic	false
CAH	CD1	LEU- 561	3.6	0	Hydrophobic	false
CAA	CG	ARG- 562	4.16	0	Hydrophobic	false
N3	O	HOH- 680	3.1	163.17	H-Bond (Ligand Donor)	false