scPDB - 4dt8 entry

Protein Data Bank Entry:

PDB ID : 4dt8

Resolution :2.150 Å

Experimental Method : X-ray

Deposition Date : 2012-02-20

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	APH(2'')-Id
ID:	O68183_ENTCA
AC:	O68183
Organism:	Enterococcus casseliflavus
Reign:	Bacteria
TaxID:	37734
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	29.616
Number of residues:	24
Including
Standard Amino Acids:	24
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.039	381.375

% Hydrophobic	% Polar
53.98	46.02
According to VolSite

Ligand :

HET Code:	ADN
Formula:	C10H13N5O4
Molecular weight:	267.241 g/mol
DrugBank ID:	DB00640
Buried Surface Area:	53.41 %
Polar Surface area:	139.54 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	2

Mass center Coordinates

X	Y	Z
11.7439	-44.2562	7.45216

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
C5'	CB	ALA- 36	3.8	0	Hydrophobic	false
N6	O	THR- 96	3.38	133.13	H-Bond (Ligand Donor)	false
N1	N	ILE- 98	2.88	164.76	H-Bond (Protein Donor)	false
C2'	CD1	ILE- 216	3.58	0	Hydrophobic	false