scPDB - 1y6o entry

Protein Data Bank Entry:

PDB ID : 1y6o

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2004-12-06

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	82 %
B	18 %

Ligand binding site composition:

B-Factor:	18.967
Number of residues:	29
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	2
Water Molecules:	0
Cofactors:
Metals:	CA

Cavity properties

Ligandability	Volume (Å3)
0.873	516.375

% Hydrophobic	% Polar
57.52	42.48
According to VolSite

Ligand :

HET Code:	MJI
Formula:	C22H43F3O6P
Molecular weight:	491.542 g/mol
DrugBank ID:	-
Buried Surface Area:	63.76 %
Polar Surface area:	86.86 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	0
Rings:	0
Aromatic rings:	0
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	24

Mass center Coordinates

X	Y	Z
0.591647	-5.86518	38.7167

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
F31	CD1	LEU- 2	3.52	0	Hydrophobic	false
C11	CD2	LEU- 2	4.01	0	Hydrophobic	false
F31	CD2	PHE- 5	3.91	0	Hydrophobic	false
F33	CD2	PHE- 5	4.34	0	Hydrophobic	false
C2P	CE2	PHE- 5	3.96	0	Hydrophobic	false
F33	CG1	ILE- 9	4.37	0	Hydrophobic	false
F32	CB	PRO- 18	3.35	0	Hydrophobic	false
F32	CD2	LEU- 19	3.43	0	Hydrophobic	false
F33	CB	PHE- 22	4.48	0	Hydrophobic	false
C3	CB	ASN- 23	4.18	0	Hydrophobic	false
C31	CB	ASN- 23	3.75	0	Hydrophobic	false
O21	N	GLY- 30	2.77	160.58	H-Bond (Protein Donor)	false
C1	CG	LEU- 31	4.25	0	Hydrophobic	false
C11	CG	LEU- 31	3.62	0	Hydrophobic	false
C2P	SG	CYS- 45	4.15	0	Hydrophobic	false
C2	CZ	TYR- 69	4.44	0	Hydrophobic	false
O22	OH	TYR- 69	2.61	165.54	H-Bond (Protein Donor)	false
C2P	CZ	PHE- 106	4.18	0	Hydrophobic	false
O21	CA	CA- 207	2.69	0	Metal Acceptor	false