scPDB - 2xyr entry

Protein Data Bank Entry:

PDB ID : 2xyr

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2010-11-18

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Replicase polyprotein 1ab
ID:	R1AB_CVHSA
AC:	P0C6X7
Organism:	Human SARS coronavirus
Reign:	Viruses
TaxID:	227859
EC Number:	2.1.1

Chains:

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

Ligand binding site composition:

B-Factor:	50.898
Number of residues:	31
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.123	435.375

% Hydrophobic	% Polar
36.43	63.57
According to VolSite

Ligand :

HET Code:	SFG
Formula:	C15H24N7O5
Molecular weight:	382.395 g/mol
DrugBank ID:	DB01910
Buried Surface Area:	64.63 %
Polar Surface area:	214.71 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	5
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	2
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
46.2293	62.6894	-2.55563

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
OXT	ND2	ASN- 43	2.57	135.26	H-Bond (Protein Donor)	false
N	O	GLY- 71	2.85	162.73	H-Bond (Ligand Donor)	false
CB	CB	SER- 74	4.2	0	Hydrophobic	false
O	N	GLY- 81	3	145.76	H-Bond (Protein Donor)	false
O3'	OD1	ASP- 99	3.25	125.14	H-Bond (Ligand Donor)	false
O2'	OD2	ASP- 99	3.28	149.34	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 99	2.73	148.24	H-Bond (Ligand Donor)	false
N3	N	LEU- 100	3.34	134.16	H-Bond (Protein Donor)	false
N1	N	CYS- 115	3.17	163.58	H-Bond (Protein Donor)	false
N	OD2	ASP- 130	2.68	167.12	H-Bond (Ligand Donor)	false
N	OD2	ASP- 130	2.68	0	Ionic (Ligand Cationic)	false
CG	CB	ASP- 130	4.34	0	Hydrophobic	false
C1'	CG	MET- 131	4.31	0	Hydrophobic	false
C5'	CB	TYR- 132	4.21	0	Hydrophobic	false
O4'	N	TYR- 132	3.4	149.16	H-Bond (Protein Donor)	false