scPDB - 1ddt entry

Protein Data Bank Entry:

PDB ID : 1ddt

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 1994-03-01

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:	20.811
Number of residues:	36
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.001	644.625

% Hydrophobic	% Polar
52.88	47.12
According to VolSite

Ligand :

HET Code:	APU
Formula:	C19H22N7O15P2
Molecular weight:	650.363 g/mol
DrugBank ID:	DB01792
Buried Surface Area:	55.67 %
Polar Surface area:	348.81 Å2

Number of
H-Bond Acceptors:	19
H-Bond Donors:	5
Rings:	5
Aromatic rings:	2
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
16.8908	34.5122	40.9554

Binding mode :

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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	2.74	143.6	H-Bond (Ligand Donor)	false
O4U	N	GLY- 22	2.88	163.65	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 24	3.16	165.77	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 24	3.16	0	Ionic (Protein Cationic)	false
N6A	O	GLY- 34	3.18	157.37	H-Bond (Ligand Donor)	false
N1A	N	GLN- 36	3.02	172.63	H-Bond (Protein Donor)	false
C5B	CG	PRO- 38	4.09	0	Hydrophobic	false
O2X	OG1	THR- 42	2.85	158.28	H-Bond (Protein Donor)	false
O2X	N	GLY- 44	2.85	136.52	H-Bond (Protein Donor)	false
C1D	CB	TYR- 54	4.38	0	Hydrophobic	false
C1D	CE1	TYR- 65	3.86	0	Hydrophobic	false
C5B	CH2	TRP- 153	4.05	0	Hydrophobic	false