scPDB - 1lpc entry

Protein Data Bank Entry:

PDB ID : 1lpc

Resolution :1.700 Å

Experimental Method : X-ray

Deposition Date : 2002-05-07

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Antiviral protein DAP-30
ID:	RIP0_DIACA
AC:	P24476
Organism:	Dianthus caryophyllus
Reign:	Eukaryota
TaxID:	3570
EC Number:	3.2.2.22

Chains:

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

Ligand binding site composition:

B-Factor:	13.089
Number of residues:	26
Including
Standard Amino Acids:	25
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.094	270.000

% Hydrophobic	% Polar
38.75	61.25
According to VolSite

Ligand :

HET Code:	CMP
Formula:	C10H11N5O6P
Molecular weight:	328.198 g/mol
DrugBank ID:	DB02527
Buried Surface Area:	66.3 %
Polar Surface area:	167.48 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	2
Rings:	4
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	1

Mass center Coordinates

X	Y	Z
68.8867	-14.8007	-5.77141

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
C2'	CZ	TYR- 73	3.59	0	Hydrophobic	false
N6	O	VAL- 74	3.42	152.68	H-Bond (Ligand Donor)	false
N1	N	VAL- 74	2.91	166.95	H-Bond (Protein Donor)	false
N6	O	GLU- 119	3.01	166.42	H-Bond (Ligand Donor)	false
C1'	CE1	TYR- 121	3.95	0	Hydrophobic	false
N3	NH2	ARG- 180	3.37	142.92	H-Bond (Protein Donor)	false
N3	NH1	ARG- 180	3.1	159.09	H-Bond (Protein Donor)	false
O2P	OG	SER- 210	3.12	145.8	H-Bond (Protein Donor)	false
O2P	N	SER- 210	2.89	168.97	H-Bond (Protein Donor)	false
O2'	O	HOH- 950	2.77	163.79	H-Bond (Ligand Donor)	false