scPDB - 4pb2 entry

Protein Data Bank Entry:

PDB ID : 4pb2

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2014-04-11

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Nucleoside permease
ID:	Q9KPL5_VIBCH
AC:	Q9KPL5
Organism:	Vibrio cholerae serotype O1
Reign:	Bacteria
TaxID:	243277
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	43.258
Number of residues:	30
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.086	421.875

% Hydrophobic	% Polar
52.80	47.20
According to VolSite

Ligand :

HET Code:	5UD
Formula:	C9H11FN2O6
Molecular weight:	262.192 g/mol
DrugBank ID:	DB01629
Buried Surface Area:	62.92 %
Polar Surface area:	119.33 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	4
Rings:	2
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	2

Mass center Coordinates

X	Y	Z
51.3299	-19.6601	-7.00961

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
O2	NE2	GLN- 154	2.92	165.95	H-Bond (Protein Donor)	false
F5	CB	ALA- 185	4.43	0	Hydrophobic	false
F5	CG2	VAL- 188	3.86	0	Hydrophobic	false
F5	CD1	LEU- 259	3.7	0	Hydrophobic	false
C5'	CB	ASN- 331	4.15	0	Hydrophobic	false
O3'	OE1	GLU- 332	2.71	172.45	H-Bond (Ligand Donor)	false
O5'	OE2	GLU- 332	2.52	176.33	H-Bond (Ligand Donor)	false
C5'	CB	PHE- 333	4.02	0	Hydrophobic	false
F5	CZ	PHE- 366	3.64	0	Hydrophobic	false
C2'	CG	PHE- 366	3.76	0	Hydrophobic	false
C3'	CD1	PHE- 366	3.6	0	Hydrophobic	false
O3'	ND2	ASN- 368	2.91	141.09	H-Bond (Protein Donor)	false
O2'	OG	SER- 371	2.6	152.84	H-Bond (Ligand Donor)	false
N3	O	HOH- 615	2.84	168.1	H-Bond (Ligand Donor)	false
O4	O	HOH- 638	2.98	162.96	H-Bond (Protein Donor)	false