scPDB - 3m4p entry

Protein Data Bank Entry:

PDB ID : 3m4p

Resolution :2.830 Å

Experimental Method : X-ray

Deposition Date : 2010-03-11

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Asparaginyl-tRNA synthetase, putative
ID:	C4LWW8_ENTHI
AC:	C4LWW8
Organism:	Entamoeba histolytica
Reign:	Eukaryota
TaxID:	5759
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	62.948
Number of residues:	44
Including
Standard Amino Acids:	44
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.641	783.000

% Hydrophobic	% Polar
38.79	61.21
According to VolSite

Ligand :

HET Code:	4AD
Formula:	C14H20N7O9P
Molecular weight:	461.324 g/mol
DrugBank ID:	-
Buried Surface Area:	71.74 %
Polar Surface area:	275.51 Å2

Number of
H-Bond Acceptors:	13
H-Bond Donors:	5
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
15.0765	-5.62797	66.1072

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	OG	SER- 204	3.44	156.02	H-Bond (Ligand Donor)	false
N	OE1	GLN- 206	2.53	158.18	H-Bond (Ligand Donor)	false
CB	CB	GLN- 206	4.29	0	Hydrophobic	false
N1	N	LEU- 237	2.83	132.32	H-Bond (Protein Donor)	false
N6	O	LEU- 237	2.93	151.99	H-Bond (Ligand Donor)	false
C1'	CE1	TYR- 240	4.18	0	Hydrophobic	false
DuAr	DuAr	TYR- 240	3.74	0	Aromatic Face/Face	false
CB	CG	GLU- 244	4.19	0	Hydrophobic	false
O3'	OE2	GLU- 374	2.69	164.11	H-Bond (Ligand Donor)	false
O2'	O	GLU- 374	2.81	154.06	H-Bond (Ligand Donor)	false
OD1	NH2	ARG- 381	3.38	164.2	H-Bond (Protein Donor)	false
C2'	CD	ARG- 425	4.15	0	Hydrophobic	false