scPDB - 4emr entry

Protein Data Bank Entry:

PDB ID : 4emr

Resolution :1.750 Å

Experimental Method : X-ray

Deposition Date : 2012-04-12

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:	24.221
Number of residues:	30
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.059	320.625

% Hydrophobic	% Polar
43.16	56.84
According to VolSite

Ligand :

HET Code:	MGP
Formula:	C11H15N5O14P3
Molecular weight:	534.183 g/mol
DrugBank ID:	DB02716
Buried Surface Area:	57.99 %
Polar Surface area:	326.55 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	4
Rings:	3
Aromatic rings:	1
Anionic atoms:	4
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
-16.6629	-17.2378	-7.1353

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
C2'	CE2	TYR- 70	3.97	0	Hydrophobic	false
CM7	CE1	TYR- 70	3.85	0	Hydrophobic	false
DuAr	DuAr	TYR- 70	3.33	0	Aromatic Face/Face	false
N2	O	ILE- 71	2.64	122.99	H-Bond (Ligand Donor)	false
N1	OE1	GLU- 85	2.98	144.75	H-Bond (Ligand Donor)	false
N1	OE2	GLU- 85	2.83	130.13	H-Bond (Ligand Donor)	false
N2	OE1	GLU- 85	2.89	148.77	H-Bond (Ligand Donor)	false
C5'	CB	ASN- 110	4.47	0	Hydrophobic	false
O2A	N	TYR- 111	2.73	159	H-Bond (Protein Donor)	false
O5'	N	TYR- 111	3.33	137.29	H-Bond (Protein Donor)	false
C5'	CG	TYR- 111	3.47	0	Hydrophobic	false
C4'	CZ	TYR- 111	4.04	0	Hydrophobic	false
C3'	CE2	TYR- 111	3.87	0	Hydrophobic	false
C4'	CG2	ILE- 155	3.94	0	Hydrophobic	false
O3'	NH1	ARG- 163	2.96	154.49	H-Bond (Protein Donor)	false
O2'	NH2	ARG- 163	2.88	134.08	H-Bond (Protein Donor)	false
O2'	NH1	ARG- 163	3.14	126.16	H-Bond (Protein Donor)	false
O3C	N	SER- 193	3.32	167.41	H-Bond (Protein Donor)	false
O2A	O	HOH- 592	2.59	164.57	H-Bond (Protein Donor)	false