scPDB - 2b04 entry

Protein Data Bank Entry:

PDB ID : 2b04

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2005-09-12

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Phospholipase A2, major isoenzyme
ID:	PA21B_PIG
AC:	P00592
Organism:	Sus scrofa
Reign:	Eukaryota
TaxID:	9823
EC Number:	3.1.1.4

Chains:

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

Ligand binding site composition:

B-Factor:	50.312
Number of residues:	25
Including
Standard Amino Acids:	24
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	CA

Cavity properties

Ligandability	Volume (Å3)
1.158	627.750

% Hydrophobic	% Polar
61.29	38.71
According to VolSite

Ligand :

HET Code:	CHO
Formula:	C26H42NO5
Molecular weight:	448.615 g/mol
DrugBank ID:	DB02123
Buried Surface Area:	51.29 %
Polar Surface area:	109.69 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	3
Rings:	4
Aromatic rings:	0
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
3.81397	34.5397	4.11975

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	CD1	LEU- 2	3.84	0	Hydrophobic	false
C1	CE2	PHE- 5	3.67	0	Hydrophobic	false
C2	CD2	PHE- 5	4.42	0	Hydrophobic	false
C11	CE2	PHE- 5	4.47	0	Hydrophobic	false
C19	CE2	PHE- 5	4.08	0	Hydrophobic	false
C2	CG	ARG- 6	4.03	0	Hydrophobic	false
O3	NE	ARG- 6	3.08	168.32	H-Bond (Protein Donor)	false
C21	CG2	ILE- 9	3.83	0	Hydrophobic	false
C11	CD1	ILE- 9	3.38	0	Hydrophobic	false
C21	CD1	ILE- 13	3.75	0	Hydrophobic	false
C2	CD2	PHE- 22	4.26	0	Hydrophobic	false
C4	CB	PHE- 22	4.23	0	Hydrophobic	false
C9	CG	PHE- 22	4.48	0	Hydrophobic	false
C12	CE1	PHE- 22	3.89	0	Hydrophobic	false
C21	CE1	PHE- 22	4.41	0	Hydrophobic	false
C14	CD1	PHE- 22	4.19	0	Hydrophobic	false
O7	O	ASN- 23	2.85	136.83	H-Bond (Ligand Donor)	false
C15	CB	TYR- 25	3.62	0	Hydrophobic	false
C15	CB	CYS- 29	4.01	0	Hydrophobic	false
C18	SG	CYS- 29	4.05	0	Hydrophobic	false
C8	CB	CYS- 29	4.09	0	Hydrophobic	false
C16	CD2	LEU- 41	3.89	0	Hydrophobic	false
C18	CD1	LEU- 41	4.1	0	Hydrophobic	false
C20	CD1	LEU- 41	4.3	0	Hydrophobic	false
C22	CD2	LEU- 41	4.34	0	Hydrophobic	false
C18	SG	CYS- 45	3.79	0	Hydrophobic	false
C18	CZ	PHE- 106	3.57	0	Hydrophobic	false
C21	CB	PHE- 106	4.21	0	Hydrophobic	false
C11	CE2	PHE- 106	3.73	0	Hydrophobic	false
C16	CE2	TYR- 111	4.04	0	Hydrophobic	false
C22	CD2	TYR- 111	3.79	0	Hydrophobic	false