scPDB - 3u8f entry

Protein Data Bank Entry:

PDB ID : 3u8f

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2011-10-17

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Ribosome inactivating protein
ID:	D9J2T9_MOMBA
AC:	D9J2T9
Organism:	Momordica balsamina
Reign:	Eukaryota
TaxID:	3672
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	28.505
Number of residues:	23
Including
Standard Amino Acids:	23
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.226	327.375

% Hydrophobic	% Polar
48.45	51.55
According to VolSite

Ligand :

HET Code:	FGM
Formula:	C19H37O3
Molecular weight:	313.495 g/mol
DrugBank ID:	-
Buried Surface Area:	53.54 %
Polar Surface area:	60.36 Å2

Number of
H-Bond Acceptors:	3
H-Bond Donors:	1
Rings:	0
Aromatic rings:	0
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	16

Mass center Coordinates

X	Y	Z
-7.865	21.6641	4.73395

Binding mode :

What is Poseview ?

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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
CCJ	CE2	TYR- 70	4.39	0	Hydrophobic	false
CBZ	CD1	TYR- 70	3.94	0	Hydrophobic	false
CCC	CB	TYR- 70	3.27	0	Hydrophobic	false
CCG	CD2	TYR- 70	3.42	0	Hydrophobic	false
CCD	CB	ILE- 71	4.46	0	Hydrophobic	false
OCR	N	ILE- 71	2.53	174.22	H-Bond (Protein Donor)	false
CCB	CE	MET- 72	4.29	0	Hydrophobic	false
CCD	CE	MET- 72	4.09	0	Hydrophobic	false
CCD	CE2	PHE- 83	4.42	0	Hydrophobic	false
CBW	CB	SER- 108	4.15	0	Hydrophobic	false
OCF	O	GLY- 109	2.52	156.35	H-Bond (Ligand Donor)	false
CCM	CB	ASN- 110	3.57	0	Hydrophobic	false
CBX	CB	ASN- 110	3.54	0	Hydrophobic	false
CCI	CE2	TYR- 111	4.37	0	Hydrophobic	false
CCJ	CD2	TYR- 111	4.44	0	Hydrophobic	false
CCL	CD2	TYR- 111	3.59	0	Hydrophobic	false
CCM	CB	TYR- 111	4.36	0	Hydrophobic	false
CCE	CD1	ILE- 155	4.41	0	Hydrophobic	false
CCH	CG2	ILE- 155	3.61	0	Hydrophobic	false
OCS	CZ	ARG- 163	3.99	0	Ionic (Protein Cationic)	false