scPDB - 3u8h entry

Protein Data Bank Entry:

PDB ID : 3u8h

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2011-10-17

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:	35.680
Number of residues:	42
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	2
Water Molecules:	1
Cofactors:
Metals:	CA

Cavity properties

Ligandability	Volume (Å3)
0.872	1667.250

% Hydrophobic	% Polar
52.63	47.37
According to VolSite

Ligand :

HET Code:	BHP
Formula:	C31H36NO4
Molecular weight:	486.622 g/mol
DrugBank ID:	DB04287
Buried Surface Area:	63.6 %
Polar Surface area:	78.46 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	1
Rings:	3
Aromatic rings:	3
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	16

Mass center Coordinates

X	Y	Z
20.6589	-6.88158	-11.0119

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
C3	CD2	LEU- 2	4.16	0	Hydrophobic	false
C18	CD2	LEU- 2	3.87	0	Hydrophobic	false
C9	CE2	PHE- 5	4.08	0	Hydrophobic	false
C4	CB	PHE- 5	4.17	0	Hydrophobic	false
C11	CE2	PHE- 5	4.05	0	Hydrophobic	false
C3	CB	HIS- 6	3.92	0	Hydrophobic	false
C8	CD1	ILE- 9	4.3	0	Hydrophobic	false
C5	CD1	ILE- 9	3.72	0	Hydrophobic	false
C5	CB	ALA- 17	3.73	0	Hydrophobic	false
C1	CB	ALA- 18	4.41	0	Hydrophobic	false
C3	CD2	LEU- 19	4.38	0	Hydrophobic	false
C8	CB	TYR- 21	3.59	0	Hydrophobic	false
C22	CZ	PHE- 23	3.39	0	Hydrophobic	false
C10	CB	CYS- 28	4.26	0	Hydrophobic	false
O1	N	GLY- 29	2.79	139.94	H-Bond (Protein Donor)	false
C20	CG2	VAL- 30	4.47	0	Hydrophobic	false
C25	CG2	VAL- 30	3.27	0	Hydrophobic	false
C26	CG2	VAL- 30	3.34	0	Hydrophobic	false
O4T	N	GLY- 31	2.84	163.21	H-Bond (Protein Donor)	false
C12	CB	CYS- 44	3.72	0	Hydrophobic	false
C10	SG	CYS- 44	4.24	0	Hydrophobic	false
C12	CB	HIS- 47	4.03	0	Hydrophobic	false
N	ND1	HIS- 47	2.81	157.84	H-Bond (Ligand Donor)	false
C29	CB	ASP- 48	4.42	0	Hydrophobic	false
C15	CE2	TYR- 51	3.55	0	Hydrophobic	false
C29	CD2	TYR- 51	3.84	0	Hydrophobic	false
O1	CA	CA- 127	2.32	0	Metal Acceptor	false
O3	CA	CA- 127	2.29	0	Metal Acceptor	false