scPDB - 3ewr entry

Protein Data Bank Entry:

PDB ID : 3ewr

Resolution :2.010 Å

Experimental Method : X-ray

Deposition Date : 2008-10-16

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Replicase polyprotein 1a
ID:	R1A_CVH22
AC:	P0C6U2
Organism:	Human coronavirus 229E
Reign:	Viruses
TaxID:	11137
EC Number:	3.4.22

Chains:

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

Ligand binding site composition:

B-Factor:	24.029
Number of residues:	40
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.791	408.375

% Hydrophobic	% Polar
61.98	38.02
According to VolSite

Ligand :

HET Code:	APR
Formula:	C15H21N5O14P2
Molecular weight:	557.300 g/mol
DrugBank ID:	-
Buried Surface Area:	69.85 %
Polar Surface area:	316.8 Å2

Number of
H-Bond Acceptors:	18
H-Bond Donors:	6
Rings:	4
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
12.6839	-1.74333	16.4702

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
N1	N	VAL- 20	3.14	128.25	H-Bond (Protein Donor)	false
O3D	ND2	ASN- 37	2.78	159.02	H-Bond (Protein Donor)	false
C3D	CB	ASN- 37	3.78	0	Hydrophobic	false
C1'	CB	LEU- 46	4.24	0	Hydrophobic	false
O1A	N	LEU- 46	2.87	169.84	H-Bond (Protein Donor)	false
C2D	CB	ALA- 47	3.77	0	Hydrophobic	false
C4'	CB	PRO- 120	3.88	0	Hydrophobic	false
O1B	N	SER- 123	2.96	132.79	H-Bond (Protein Donor)	false
C3'	SG	CYS- 124	4.08	0	Hydrophobic	false
O2B	N	GLY- 125	2.64	138.39	H-Bond (Protein Donor)	false
O2A	N	ILE- 126	2.84	162.94	H-Bond (Protein Donor)	false
C1D	CG2	ILE- 126	4.45	0	Hydrophobic	false
C4D	CG1	ILE- 126	3.72	0	Hydrophobic	false
O2B	N	PHE- 127	3.1	167.95	H-Bond (Protein Donor)	false
O5D	N	PHE- 127	3.42	127.29	H-Bond (Protein Donor)	false
C5D	CD2	PHE- 127	3.81	0	Hydrophobic	false
C3D	CZ	PHE- 127	3.98	0	Hydrophobic	false
C4D	CE1	PHE- 127	3.88	0	Hydrophobic	false
C2'	CB	TYR- 152	3.74	0	Hydrophobic	false
O2'	OE1	GLU- 156	2.93	156.84	H-Bond (Ligand Donor)	false
O3'	OE2	GLU- 156	2.57	157.45	H-Bond (Ligand Donor)	false
O3A	O	HOH- 204	3.37	140.09	H-Bond (Protein Donor)	false
O2D	O	HOH- 218	2.6	179.99	H-Bond (Protein Donor)	false