scPDB - 3gqo entry

Protein Data Bank Entry:

PDB ID : 3gqo

Resolution :2.600 Å

Experimental Method : X-ray

Deposition Date : 2009-03-24

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Non-structural polyprotein
ID:	POLN_EEVVP
AC:	P36328
Organism:	Venezuelan equine encephalitis virus
Reign:	Viruses
TaxID:	36385
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	16.468
Number of residues:	38
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.708	556.875

% Hydrophobic	% Polar
49.09	50.91
According to VolSite

Ligand :

HET Code:	APR
Formula:	C15H21N5O14P2
Molecular weight:	557.300 g/mol
DrugBank ID:	-
Buried Surface Area:	73.3 %
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
-8.658	15.393	37.5305

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
N6	OD1	ASP- 10	2.67	177.34	H-Bond (Ligand Donor)	false
N1	N	ILE- 11	2.95	171.21	H-Bond (Protein Donor)	false
C5D	CB	ALA- 22	4.29	0	Hydrophobic	false
O3D	ND2	ASN- 24	2.75	157.28	H-Bond (Protein Donor)	false
C3D	CB	ASN- 24	3.9	0	Hydrophobic	false
O1D	N	GLY- 31	2.68	129.69	H-Bond (Protein Donor)	false
O1D	N	GLY- 32	2.72	121.62	H-Bond (Protein Donor)	false
C1'	CG1	VAL- 33	4.36	0	Hydrophobic	false
C5'	CG1	VAL- 33	4.26	0	Hydrophobic	false
O1A	N	VAL- 33	2.92	162.89	H-Bond (Protein Donor)	false
C2D	CB	CYS- 34	3.72	0	Hydrophobic	false
O1B	N	SER- 110	2.74	155.57	H-Bond (Protein Donor)	false
C3'	CB	THR- 111	4.15	0	Hydrophobic	false
O3'	OG1	THR- 111	2.6	156.9	H-Bond (Ligand Donor)	false
O2B	N	GLY- 112	2.75	139.02	H-Bond (Protein Donor)	false
O2A	N	ILE- 113	2.7	166.79	H-Bond (Protein Donor)	false
C1D	CD1	ILE- 113	3.74	0	Hydrophobic	false
C4D	CB	ILE- 113	3.91	0	Hydrophobic	false
O2B	N	PHE- 114	2.85	169.24	H-Bond (Protein Donor)	false
C5D	CD2	PHE- 114	3.61	0	Hydrophobic	false
C3D	CZ	PHE- 114	3.61	0	Hydrophobic	false
C4D	CE1	PHE- 114	3.59	0	Hydrophobic	false
O1B	O	HOH- 208	2.97	179.96	H-Bond (Protein Donor)	false