scPDB - 4p5f entry

Protein Data Bank Entry:

PDB ID : 4p5f

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2014-03-17

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Inosine-uridine nucleoside N-ribohydrolase
ID:	Q5GUA3_XANOR
AC:	Q5GUA3
Organism:	Xanthomonas oryzae pv. oryzae
Reign:	Bacteria
TaxID:	291331
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	27.088
Number of residues:	46
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	1
Water Molecules:	3
Cofactors:
Metals:	CA

Cavity properties

Ligandability	Volume (Å3)
0.391	418.500

% Hydrophobic	% Polar
51.61	48.39
According to VolSite

Ligand :

HET Code:	AR6
Formula:	C15H21N5O14P2
Molecular weight:	557.300 g/mol
DrugBank ID:	DB02059
Buried Surface Area:	77.79 %
Polar Surface area:	316.8 Å2

Number of
H-Bond Acceptors:	18
H-Bond Donors:	6
Rings:	4
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
3.63083	42.6645	-8.31108

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
O2'	OD2	ASP- 120	2.89	160.79	H-Bond (Ligand Donor)	false
C2D	CB	ASP- 120	4.1	0	Hydrophobic	false
O2D	OD1	ASP- 122	2.54	128.57	H-Bond (Ligand Donor)	false
O2D	OD2	ASP- 122	3.18	162.18	H-Bond (Ligand Donor)	false
C5D	SD	MET- 259	3.53	0	Hydrophobic	false
O2A	NH1	ARG- 277	2.73	134.95	H-Bond (Protein Donor)	false
O2A	NH2	ARG- 277	2.69	136.71	H-Bond (Protein Donor)	false
O2B	NH1	ARG- 277	3.36	129.61	H-Bond (Protein Donor)	false
O2A	CZ	ARG- 277	3.1	0	Ionic (Protein Cationic)	false
C1D	CD2	TYR- 279	4.06	0	Hydrophobic	false
C3'	CB	TYR- 279	4.07	0	Hydrophobic	false
C4D	CB	TYR- 279	4.47	0	Hydrophobic	false
O2B	N	TYR- 279	2.78	166.94	H-Bond (Protein Donor)	false
O1D	OD1	ASN- 280	3	158.71	H-Bond (Ligand Donor)	false
O3D	ND2	ASN- 280	2.84	162.27	H-Bond (Protein Donor)	false
O1A	OH	TYR- 311	2.68	136.13	H-Bond (Protein Donor)	false
C1'	CD2	LEU- 345	3.82	0	Hydrophobic	false
C4'	CD1	LEU- 345	4.14	0	Hydrophobic	false
C5'	CD1	LEU- 357	3.68	0	Hydrophobic	false
C5'	CH2	TRP- 361	3.77	0	Hydrophobic	false
O1A	OH	TYR- 398	2.73	122.67	H-Bond (Protein Donor)	false
C2'	CE2	TYR- 398	4.26	0	Hydrophobic	false
C5D	CG	TYR- 398	3.68	0	Hydrophobic	false
C3D	CD2	TYR- 398	3.83	0	Hydrophobic	false
O3D	OD1	ASP- 399	2.64	154.07	H-Bond (Ligand Donor)	false
O1D	CA	CA- 501	2.74	0	Metal Acceptor	false
O2D	CA	CA- 501	2.47	0	Metal Acceptor	false
O1B	O	HOH- 645	2.75	179.96	H-Bond (Protein Donor)	false
O1B	O	HOH- 685	2.61	165.35	H-Bond (Protein Donor)	false