scPDB - 1pag entry

Protein Data Bank Entry:

PDB ID : 1pag

Resolution :2.800 Å

Experimental Method : X-ray

Deposition Date : 1992-10-19

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Antiviral protein I
ID:	RIP1_PHYAM
AC:	P10297
Organism:	Phytolacca americana
Reign:	Eukaryota
TaxID:	3527
EC Number:	3.2.2.22

Chains:

Chain Name:	Percentage of Residues within binding site
A	88 %
B	12 %

Ligand binding site composition:

B-Factor:	12.677
Number of residues:	26
Including
Standard Amino Acids:	26
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.275	2463.750

% Hydrophobic	% Polar
43.29	56.71
According to VolSite

Ligand :

HET Code:	FMP
Formula:	C10H12N5O7P
Molecular weight:	345.205 g/mol
DrugBank ID:	DB03464
Buried Surface Area:	59.48 %
Polar Surface area:	212.4 Å2

Number of
H-Bond Acceptors:	11
H-Bond Donors:	4
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
8.24983	23.8134	24.3019

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
DuAr	DuAr	TYR- 72	3.76	0	Aromatic Face/Face	false
C2'	CZ	TYR- 72	3.54	0	Hydrophobic	false
N6	O	VAL- 73	3.25	152.75	H-Bond (Ligand Donor)	false
N1	N	VAL- 73	3.03	163.91	H-Bond (Protein Donor)	false
N7	O	SER- 121	2.73	147.07	H-Bond (Ligand Donor)	false
C5	CB	SER- 121	4.36	0	Hydrophobic	false
O2P	NH1	ARG- 122	3.43	142.78	H-Bond (Protein Donor)	false
C1'	CE2	TYR- 123	3.74	0	Hydrophobic	false
C5	CG2	ILE- 171	4.29	0	Hydrophobic	false
N3	NH2	ARG- 179	2.77	149.68	H-Bond (Protein Donor)	false