scPDB - 1tox entry

Protein Data Bank Entry:

PDB ID : 1tox

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 1995-10-06

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Diphtheria toxin
ID:	DTX_CORBE
AC:	P00588
Organism:	Corynephage beta
Reign:	Viruses
TaxID:	10703
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	18.256
Number of residues:	31
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.645	263.250

% Hydrophobic	% Polar
50.00	50.00
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	56.05 %
Polar Surface area:	343.54 Å2

Number of
H-Bond Acceptors:	18
H-Bond Donors:	6
Rings:	5
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
30.2256	-43.6596	-23.1924

Binding mode :

What is Poseview ?

2D View
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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
O2B	NE2	HIS- 21	2.77	154.05	H-Bond (Ligand Donor)	false
O7N	N	GLY- 22	2.78	165.38	H-Bond (Protein Donor)	false
N7N	O	GLY- 22	3.04	173.86	H-Bond (Ligand Donor)	false
O2B	OG1	THR- 23	2.73	153.22	H-Bond (Protein Donor)	false
N6A	O	GLY- 34	2.92	145.82	H-Bond (Ligand Donor)	false
N1A	N	GLN- 36	2.94	172.66	H-Bond (Protein Donor)	false
C5B	CG	PRO- 38	4.37	0	Hydrophobic	false
C3D	CG	TYR- 54	3.87	0	Hydrophobic	false
C2D	CD2	TYR- 54	3.73	0	Hydrophobic	false
C5N	CB	TYR- 54	4.01	0	Hydrophobic	false
C5N	CB	THR- 56	4.08	0	Hydrophobic	false
C4D	CE1	TYR- 65	4.22	0	Hydrophobic	false
C3N	CB	TYR- 65	4.4	0	Hydrophobic	false
DuAr	DuAr	TYR- 65	3.68	0	Aromatic Face/Face	false
O2D	OE1	GLU- 148	3.39	138.66	H-Bond (Ligand Donor)	false
C5N	CG	GLU- 148	4.28	0	Hydrophobic	false