scPDB - 4dne entry

Protein Data Bank Entry:

PDB ID : 4dne

Resolution :1.880 Å

Experimental Method : X-ray

Deposition Date : 2012-02-08

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Streptavidin
ID:	SAV_STRAV
AC:	P22629
Organism:	Streptomyces avidinii
Reign:	Bacteria
TaxID:	1895
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	11.505
Number of residues:	30
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.698	280.125

% Hydrophobic	% Polar
59.04	40.96
According to VolSite

Ligand :

HET Code:	DTB
Formula:	C10H17N2O3
Molecular weight:	213.254 g/mol
DrugBank ID:	DB03775
Buried Surface Area:	75 %
Polar Surface area:	81.25 Å2

Number of
H-Bond Acceptors:	3
H-Bond Donors:	2
Rings:	1
Aromatic rings:	0
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
-6.5872	32.0537	12.6213

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
O	ND2	ASN- 23	3.04	157.06	H-Bond (Protein Donor)	false
O	OG	SER- 27	2.66	152.45	H-Bond (Protein Donor)	false
O	OH	TYR- 43	2.74	167.06	H-Bond (Protein Donor)	false
N2	OG1	THR- 45	3.01	140.59	H-Bond (Ligand Donor)	false
CD	CB	THR- 45	4.17	0	Hydrophobic	false
CB	CG2	THR- 45	4.38	0	Hydrophobic	false
OI1	N	ASN- 49	2.79	176.23	H-Bond (Protein Donor)	false
CB	CB	ALA- 50	4.09	0	Hydrophobic	false
CG	CE2	TRP- 79	3.78	0	Hydrophobic	false
CE	CZ2	TRP- 79	3.93	0	Hydrophobic	false
CB	CD2	TRP- 79	3.81	0	Hydrophobic	false
CA	CB	ALA- 86	3.89	0	Hydrophobic	false
OI2	OG	SER- 88	2.77	174.17	H-Bond (Protein Donor)	false
CT	CG2	THR- 90	3.7	0	Hydrophobic	false
CT	CZ2	TRP- 92	3.75	0	Hydrophobic	false
CT	CE2	TRP- 108	3.41	0	Hydrophobic	false
CE	CD2	LEU- 110	4.27	0	Hydrophobic	false
CG	CD2	LEU- 110	3.91	0	Hydrophobic	false
N1	OD2	ASP- 128	2.9	149.81	H-Bond (Ligand Donor)	false