scPDB - 2i4n entry

Protein Data Bank Entry:

PDB ID : 2i4n

Resolution :2.850 Å

Experimental Method : X-ray

Deposition Date : 2006-08-22

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Proline--tRNA ligase
ID:	SYP_RHOPA
AC:	Q6N5P6
Organism:	Rhodopseudomonas palustris
Reign:	Bacteria
TaxID:	258594
EC Number:	6.1.1.15

Chains:

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

Ligand binding site composition:

B-Factor:	47.367
Number of residues:	40
Including
Standard Amino Acids:	40
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.158	918.000

% Hydrophobic	% Polar
34.56	65.44
According to VolSite

Ligand :

HET Code:	5CA
Formula:	C13H19N7O7S2
Molecular weight:	449.463 g/mol
DrugBank ID:	DB02684
Buried Surface Area:	79.15 %
Polar Surface area:	268.66 Å2

Number of
H-Bond Acceptors:	12
H-Bond Donors:	5
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
24.6738	21.5245	-32.2687

Binding mode :

What is Poseview ?

2D View
3D View

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
N	OE2	GLU- 111	2.55	153.79	H-Bond (Ligand Donor)	false
N	OE2	GLU- 111	2.55	0	Ionic (Ligand Cationic)	false
N	OE1	GLU- 111	3.84	0	Ionic (Ligand Cationic)	false
O	NH2	ARG- 140	2.78	130.73	H-Bond (Protein Donor)	false
O1S	NH2	ARG- 140	2.86	141.41	H-Bond (Protein Donor)	false
O1S	NH1	ARG- 140	2.83	143.02	H-Bond (Protein Donor)	false
N6	OE1	GLU- 142	3.35	134.73	H-Bond (Ligand Donor)	false
N6	O	GLY- 152	2.87	155.8	H-Bond (Ligand Donor)	false
C1'	CE1	PHE- 155	3.95	0	Hydrophobic	false
DuAr	DuAr	PHE- 155	3.49	0	Aromatic Face/Face	false
SG	SD	MET- 157	4.42	0	Hydrophobic	false
C5'	SD	MET- 157	3.72	0	Hydrophobic	false
C4'	CG	MET- 157	4.28	0	Hydrophobic	false
SG	CB	ASP- 159	3.44	0	Hydrophobic	false
SG	CE1	TYR- 161	4	0	Hydrophobic	false
O3'	OE2	GLU- 282	2.68	159.69	H-Bond (Ligand Donor)	false
C3'	CG	GLU- 282	4.15	0	Hydrophobic	false
CB	CE1	PHE- 287	3.65	0	Hydrophobic	false
SG	CB	SER- 315	3.59	0	Hydrophobic	false