scPDB - 4dt9 entry

Protein Data Bank Entry:

PDB ID : 4dt9

Resolution :2.100 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
A	100 %

Ligand binding site composition:

B-Factor:	35.133
Number of residues:	26
Including
Standard Amino Acids:	25
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.420	2106.000

% Hydrophobic	% Polar
42.31	57.69
According to VolSite

Ligand :

HET Code:	GMP
Formula:	C10H13N5O5
Molecular weight:	283.241 g/mol
DrugBank ID:	DB02857
Buried Surface Area:	60.43 %
Polar Surface area:	155.22 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	5
Rings:	3
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	2

Mass center Coordinates

X	Y	Z
2.4932	8.54065	29.4187

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
C1'	CB	SER- 28	4.32	0	Hydrophobic	false
C5'	CB	ALA- 36	4.07	0	Hydrophobic	false
O6	N	ILE- 98	2.92	170.28	H-Bond (Protein Donor)	false
N1	O	ILE- 98	2.7	160.7	H-Bond (Ligand Donor)	false
N2	O	ILE- 98	3.26	133.54	H-Bond (Ligand Donor)	false
C3'	CD1	ILE- 216	3.65	0	Hydrophobic	false
O5'	OD1	ASP- 217	2.78	155.09	H-Bond (Ligand Donor)	false
O3'	OD2	ASP- 217	2.71	171.68	H-Bond (Ligand Donor)	false