scPDB - 2qvd entry

Protein Data Bank Entry:

PDB ID : 2qvd

Resolution :1.930 Å

Experimental Method : X-ray

Deposition Date : 2007-08-08

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Basic phospholipase A2 VRV-PL-VIIIa
ID:	PA2B8_DABRR
AC:	P59071
Organism:	Daboia russelii
Reign:	Eukaryota
TaxID:	31159
EC Number:	3.1.1.4

Chains:

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

Ligand binding site composition:

B-Factor:	30.231
Number of residues:	19
Including
Standard Amino Acids:	19
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.546	334.125

% Hydrophobic	% Polar
62.63	37.37
According to VolSite

Ligand :

HET Code:	BER
Formula:	C20H18NO4
Molecular weight:	336.361 g/mol
DrugBank ID:	DB04115
Buried Surface Area:	36.18 %
Polar Surface area:	40.79 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	0
Rings:	5
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	2

Mass center Coordinates

X	Y	Z
21.6413	47.2807	-8.02348

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	CD2	LEU- 2	4.42	0	Hydrophobic	false
C3	CD2	LEU- 2	4.13	0	Hydrophobic	false
C12	CD1	LEU- 2	3.71	0	Hydrophobic	false
C17	CE2	PHE- 5	4.01	0	Hydrophobic	false
C9	CD1	ILE- 9	3.88	0	Hydrophobic	false
C10	CB	ALA- 18	3.47	0	Hydrophobic	false
C10	CG1	ILE- 19	4.05	0	Hydrophobic	false
C19	CD1	ILE- 19	4.13	0	Hydrophobic	false
C9	CB	TYR- 22	4.23	0	Hydrophobic	false
C4	CB	SER- 23	4.4	0	Hydrophobic	false
C17	CB	CYS- 29	4.3	0	Hydrophobic	false
O1	N	GLY- 30	3.29	156.63	H-Bond (Protein Donor)	false
C17	SG	CYS- 45	3.36	0	Hydrophobic	false
C17	CZ	PHE- 106	3.84	0	Hydrophobic	false