scPDB - 4pb1 entry

Protein Data Bank Entry:

PDB ID : 4pb1

Resolution :2.800 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:	46.247
Number of residues:	24
Including
Standard Amino Acids:	24
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.945	357.750

% Hydrophobic	% Polar
64.15	35.85
According to VolSite

Ligand :

HET Code:	RBV
Formula:	C8H12N4O5
Molecular weight:	244.205 g/mol
DrugBank ID:	DB00811
Buried Surface Area:	67.35 %
Polar Surface area:	143.72 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	4
Rings:	2
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	3

Mass center Coordinates

X	Y	Z
51.2955	-19.7554	-7.88765

Binding mode :

What is Poseview ?

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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
N3	OE1	GLU- 156	3.11	167.02	H-Bond (Ligand Donor)	false
C5'	CE	MET- 266	4.42	0	Hydrophobic	false
C4'	CB	ASN- 331	4.05	0	Hydrophobic	false
O3'	OE1	GLU- 332	2.66	168.51	H-Bond (Ligand Donor)	false
O5'	OE2	GLU- 332	2.58	168.05	H-Bond (Ligand Donor)	false
C5'	CB	PHE- 333	3.7	0	Hydrophobic	false
C2'	CG	PHE- 366	3.76	0	Hydrophobic	false
C3'	CD1	PHE- 366	3.51	0	Hydrophobic	false
O3'	ND2	ASN- 368	2.92	143.22	H-Bond (Protein Donor)	false
O2'	OG	SER- 371	2.7	130.37	H-Bond (Ligand Donor)	false
C1'	CD1	ILE- 374	4.09	0	Hydrophobic	false