scPDB - 2pau entry

Protein Data Bank Entry:

PDB ID : 2pau

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2007-03-27

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	5'-deoxynucleotidase YfbR
ID:	5DNU_ECOLI
AC:	P76491
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	46.464
Number of residues:	24
Including
Standard Amino Acids:	24
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.574	931.500

% Hydrophobic	% Polar
42.39	57.61
According to VolSite

Ligand :

HET Code:	D5M
Formula:	C10H12N5O6P
Molecular weight:	329.206 g/mol
DrugBank ID:	-
Buried Surface Area:	56.08 %
Polar Surface area:	181.31 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	2
Rings:	3
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
3.06509	20.3512	45.6168

Binding mode :

What is Poseview ?

2D View
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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
C3'	CB	ARG- 18	4.25	0	Hydrophobic	false
O1P	NH2	ARG- 18	3.34	129.06	H-Bond (Protein Donor)	false
O1P	NH1	ARG- 18	2.87	144.75	H-Bond (Protein Donor)	false
O1P	CZ	ARG- 18	3.52	0	Ionic (Protein Cationic)	false
O3'	N	TRP- 19	3	157.63	H-Bond (Protein Donor)	false
C2'	CE2	TRP- 19	3.9	0	Hydrophobic	false
C1'	CE3	TRP- 19	4.33	0	Hydrophobic	false
O3'	OD1	ASP- 77	3.37	130.87	H-Bond (Ligand Donor)	false
O4'	OG1	THR- 80	3.26	175.96	H-Bond (Protein Donor)	false
O4'	N	THR- 80	2.88	150.5	H-Bond (Protein Donor)	false