scPDB - 1kny entry

Protein Data Bank Entry:

PDB ID : 1kny

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 1995-07-07

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Kanamycin nucleotidyltransferase
ID:	KANU_STAAU
AC:	P05057
Organism:	Staphylococcus aureus
Reign:	Bacteria
TaxID:	1280
EC Number:	2.7.7

Chains:

Chain Name:	Percentage of Residues within binding site
A	86 %
B	14 %

Ligand binding site composition:

B-Factor:	31.617
Number of residues:	37
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	3
Water Molecules:	0
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.613	870.750

% Hydrophobic	% Polar
34.88	65.12
According to VolSite

Ligand :

HET Code:	APC
Formula:	C11H14N5O12P3
Molecular weight:	501.176 g/mol
DrugBank ID:	DB02596
Buried Surface Area:	55.11 %
Polar Surface area:	310.64 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
14.1029	42.8639	37.2195

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	N	SER- 39	3.21	161.75	H-Bond (Protein Donor)	false
O1B	CZ	ARG- 42	3.7	0	Ionic (Protein Cationic)	false
O3'	NH2	ARG- 42	3.12	131.55	H-Bond (Protein Donor)	false
O2G	OG	SER- 49	2.9	149.07	H-Bond (Protein Donor)	false
C5'	CG	GLU- 52	4.38	0	Hydrophobic	false
C1'	CB	GLN- 102	3.82	0	Hydrophobic	false
O2A	NZ	LYS- 149	3.38	165.16	H-Bond (Protein Donor)	false
O2A	NZ	LYS- 149	3.38	0	Ionic (Protein Cationic)	false
O1B	OG1	THR- 187	2.79	139.18	H-Bond (Protein Donor)	false
O1G	MG	MG- 603	2.24	0	Metal Acceptor	false
O2B	MG	MG- 603	2.65	0	Metal Acceptor	false