scPDB - 1ifu entry

Protein Data Bank Entry:

PDB ID : 1ifu

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 1996-07-05

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Ricin
ID:	RICI_RICCO
AC:	P02879
Organism:	Ricinus communis
Reign:	Eukaryota
TaxID:	3988
EC Number:	3.2.2.22

Chains:

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

Ligand binding site composition:

B-Factor:	19.230
Number of residues:	24
Including
Standard Amino Acids:	24
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.163	253.125

% Hydrophobic	% Polar
56.00	44.00
According to VolSite

Ligand :

HET Code:	FMC
Formula:	C10H13N5O4
Molecular weight:	267.241 g/mol
DrugBank ID:	DB02281
Buried Surface Area:	66.52 %
Polar Surface area:	150.4 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	5
Rings:	3
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	2

Mass center Coordinates

X	Y	Z
57.5738	-24.2756	96.9752

Binding mode :

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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'	CE2	TYR- 80	4.47	0	Hydrophobic	false
DuAr	DuAr	TYR- 80	3.45	0	Aromatic Face/Face	false
N1	N	VAL- 81	2.93	153.75	H-Bond (Protein Donor)	false
N6	O	VAL- 81	3.12	153.77	H-Bond (Ligand Donor)	false
N6	O	GLY- 121	3.12	150.11	H-Bond (Ligand Donor)	false
C1'	CE2	TYR- 123	3.35	0	Hydrophobic	false
C5	CD1	ILE- 172	4.09	0	Hydrophobic	false
O2'	OE2	GLU- 177	3.24	164.39	H-Bond (Ligand Donor)	false
N3	NH2	ARG- 180	3.26	138.89	H-Bond (Protein Donor)	false