scPDB - 4mx1 entry

Protein Data Bank Entry:

PDB ID : 4mx1

Resolution :1.590 Å

Experimental Method : X-ray

Deposition Date : 2013-09-25

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:	18.562
Number of residues:	30
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.454	745.875

% Hydrophobic	% Polar
36.65	63.35
According to VolSite

Ligand :

HET Code:	1MX
Formula:	C16H16N8O3
Molecular weight:	368.350 g/mol
DrugBank ID:	-
Buried Surface Area:	68.22 %
Polar Surface area:	163.48 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	5
Rings:	3
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
-24.908	11.9575	-10.5744

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
C13	CB	ASN- 78	3.99	0	Hydrophobic	false
DuAr	DuAr	TYR- 80	3.97	0	Aromatic Face/Face	false
C11	CE2	TYR- 80	2.78	0	Hydrophobic	false
N	O	VAL- 81	2.89	139.75	H-Bond (Ligand Donor)	false
N1	N	VAL- 81	3.02	150.58	H-Bond (Protein Donor)	false
N	O	GLY- 121	3.18	130	H-Bond (Ligand Donor)	false
N2	O	GLY- 121	2.67	161.38	H-Bond (Ligand Donor)	false
O1	N	TYR- 123	2.91	166.55	H-Bond (Protein Donor)	false
O	NH2	ARG- 180	2.91	137.4	H-Bond (Protein Donor)	false
N4	NH2	ARG- 180	3.43	134.01	H-Bond (Protein Donor)	false
N4	NH1	ARG- 180	3.09	145.91	H-Bond (Protein Donor)	false
N6	O	GLU- 208	3.42	152.47	H-Bond (Ligand Donor)	false
O2	N	GLY- 212	2.87	166.89	H-Bond (Protein Donor)	false
C13	CG2	VAL- 256	4.41	0	Hydrophobic	false
C14	CG1	VAL- 256	4.11	0	Hydrophobic	false
O2	O	HOH- 402	3.01	126.85	H-Bond (Protein Donor)	false
N5	O	HOH- 409	3.32	140.1	H-Bond (Ligand Donor)	false