scPDB - 4lwx entry

Protein Data Bank Entry:

PDB ID : 4lwx

Resolution :1.780 Å

Experimental Method : X-ray

Deposition Date : 2013-07-29

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:	26.098
Number of residues:	25
Including
Standard Amino Acids:	25
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.109	367.875

% Hydrophobic	% Polar
51.38	48.62
According to VolSite

Ligand :

HET Code:	MU2
Formula:	C19H31N4O11
Molecular weight:	491.470 g/mol
DrugBank ID:	-
Buried Surface Area:	49.97 %
Polar Surface area:	249.66 Å2

Number of
H-Bond Acceptors:	11
H-Bond Donors:	7
Rings:	1
Aromatic rings:	0
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	12

Mass center Coordinates

X	Y	Z
-9.09861	-22.434	-18.4102

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
O6	O	VAL- 69	2.69	143.46	H-Bond (Ligand Donor)	false
C1	CE2	TYR- 70	4.43	0	Hydrophobic	false
C20	CB	TYR- 70	3.91	0	Hydrophobic	false
C4	CD2	TYR- 70	3.82	0	Hydrophobic	false
O4	N	ILE- 71	3.02	146.9	H-Bond (Protein Donor)	false
C6	CG1	ILE- 71	4.47	0	Hydrophobic	false
C20	CE	MET- 72	3.71	0	Hydrophobic	false
C20	CD2	PHE- 83	4.04	0	Hydrophobic	false
C23	CB	SER- 108	3.71	0	Hydrophobic	false
N2	O	GLY- 109	3.49	122.54	H-Bond (Ligand Donor)	false
C8	CB	ASN- 110	3.74	0	Hydrophobic	false
C23	CB	ASN- 110	3.99	0	Hydrophobic	false
C1	CE2	TYR- 111	4.14	0	Hydrophobic	false
O7	N	TYR- 111	2.94	173.88	H-Bond (Protein Donor)	false
C1	CG2	ILE- 155	4.44	0	Hydrophobic	false
C4	CD1	ILE- 155	4.19	0	Hydrophobic	false
C5	CG2	ILE- 155	3.3	0	Hydrophobic	false
C6	CB	ALA- 159	3.65	0	Hydrophobic	false
O5	NH1	ARG- 163	3.36	157.97	H-Bond (Protein Donor)	false