scPDB - 2f2h entry

Protein Data Bank Entry:

PDB ID : 2f2h

Resolution :1.950 Å

Experimental Method : X-ray

Deposition Date : 2005-11-16

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Alpha-xylosidase
ID:	XYLS_ECOLI
AC:	P31434
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	3.2.1.177

Chains:

Chain Name:	Percentage of Residues within binding site
C	13 %
E	82 %
F	5 %

Ligand binding site composition:

B-Factor:	22.724
Number of residues:	44
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	0
Water Molecules:	5
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.048	408.375

% Hydrophobic	% Polar
47.93	52.07
According to VolSite

Ligand :

HET Code:	XTG
Formula:	C17H23NO11S
Molecular weight:	449.430 g/mol
DrugBank ID:	DB04807
Buried Surface Area:	74.71 %
Polar Surface area:	220.19 Å2

Number of
H-Bond Acceptors:	12
H-Bond Donors:	6
Rings:	3
Aromatic rings:	1
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
111.921	129.177	111.263

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
C1	CZ3	TRP- 8	3.93	0	Hydrophobic	false
C2	CD2	TRP- 8	4.31	0	Hydrophobic	false
C3	CE2	TRP- 8	4.04	0	Hydrophobic	false
C5	CZ2	TRP- 8	3.69	0	Hydrophobic	false
C14	CD1	LEU- 48	3.78	0	Hydrophobic	false
O3	OD2	ASP- 185	2.59	140.61	H-Bond (Ligand Donor)	false
O4	OD2	ASP- 185	2.58	173.8	H-Bond (Ligand Donor)	false
S6	CE2	PHE- 277	3.99	0	Hydrophobic	false
C11	CE1	PHE- 277	3.49	0	Hydrophobic	false
C10	CD1	PHE- 277	4.22	0	Hydrophobic	false
O11	OG1	THR- 278	2.75	173.63	H-Bond (Protein Donor)	false
O8	OD2	ASP- 306	2.74	162.39	H-Bond (Ligand Donor)	false
C11	SG	CYS- 307	3.72	0	Hydrophobic	false
C2	CE3	TRP- 380	4.29	0	Hydrophobic	false
C4	CZ3	TRP- 380	4.11	0	Hydrophobic	false
S6	CZ3	TRP- 380	4.14	0	Hydrophobic	false
C7	CH2	TRP- 380	4.15	0	Hydrophobic	false
C11	CH2	TRP- 380	4.05	0	Hydrophobic	false
C4	CE2	PHE- 417	3.98	0	Hydrophobic	false
C7	CZ	PHE- 417	3.73	0	Hydrophobic	false
O4	NH1	ARG- 466	2.94	157.07	H-Bond (Protein Donor)	false
O6	NH1	ARG- 466	3.13	144.89	H-Bond (Protein Donor)	false
C8	CH2	TRP- 479	4.24	0	Hydrophobic	false
O6	OD2	ASP- 482	2.97	123.86	H-Bond (Ligand Donor)	false
O6	OD1	ASP- 482	2.97	172.32	H-Bond (Ligand Donor)	false
S6	CE1	PHE- 515	4.01	0	Hydrophobic	false
C9	CZ	PHE- 515	3.8	0	Hydrophobic	false
O8	NE2	HIS- 540	2.62	149.28	H-Bond (Protein Donor)	false
O10	NZ	LYS- 543	3.95	0	Ionic (Protein Cationic)	false
O7	O	HOH- 3120	2.91	179.98	H-Bond (Protein Donor)	false
O4	O	HOH- 3152	3.32	147.75	H-Bond (Protein Donor)	false
O2	O	HOH- 3273	2.96	179.97	H-Bond (Protein Donor)	false