scPDB - 3u8d entry

Protein Data Bank Entry:

PDB ID : 3u8d

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2011-10-16

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Phospholipase A2, membrane associated
ID:	PA2GA_HUMAN
AC:	P14555
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	85 %
B	15 %

Ligand binding site composition:

B-Factor:	14.887
Number of residues:	42
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	CA

Cavity properties

Ligandability	Volume (Å3)
0.824	705.375

% Hydrophobic	% Polar
55.02	44.98
According to VolSite

Ligand :

HET Code:	U8D
Formula:	C22H25N2O5P
Molecular weight:	428.418 g/mol
DrugBank ID:	-
Buried Surface Area:	73.04 %
Polar Surface area:	130.25 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	1
Rings:	3
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
15.4962	30.097	16.4722

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
C7	CD2	LEU- 2	3.84	0	Hydrophobic	false
C15	CB	LEU- 2	4.12	0	Hydrophobic	false
C11	CE2	PHE- 5	4.12	0	Hydrophobic	false
C15	CB	PHE- 5	4.28	0	Hydrophobic	false
C20	CE2	PHE- 5	3.89	0	Hydrophobic	false
C14	CB	HIS- 6	3.57	0	Hydrophobic	false
C20	CD1	ILE- 9	3.52	0	Hydrophobic	false
C20	CB	ALA- 17	4.22	0	Hydrophobic	false
C18	CB	ALA- 18	4.18	0	Hydrophobic	false
C19	CD2	LEU- 19	3.27	0	Hydrophobic	false
C10	CB	TYR- 21	3.6	0	Hydrophobic	false
C13	CZ	PHE- 23	4.29	0	Hydrophobic	false
C10	CB	CYS- 28	4.22	0	Hydrophobic	false
C25	CG2	VAL- 30	4.24	0	Hydrophobic	false
C7	CG2	VAL- 30	3.97	0	Hydrophobic	false
O29	N	GLY- 31	2.81	141.79	H-Bond (Protein Donor)	false
C11	SG	CYS- 44	3.9	0	Hydrophobic	false
N23	ND1	HIS- 47	3.22	165.17	H-Bond (Ligand Donor)	false
C24	CD2	TYR- 51	3.9	0	Hydrophobic	false
C24	CG	LYS- 62	4.39	0	Hydrophobic	false
C10	CZ	PHE- 98	4.11	0	Hydrophobic	false
C20	CE2	PHE- 98	3.6	0	Hydrophobic	false
O22	CA	CA- 202	2.55	0	Metal Acceptor	false
O29	CA	CA- 202	2.32	0	Metal Acceptor	false