scPDB - 1db4 entry

Protein Data Bank Entry:

PDB ID : 1db4

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 1999-11-02

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	100 %

Ligand binding site composition:

B-Factor:	23.500
Number of residues:	35
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:	CA

Cavity properties

Ligandability	Volume (Å3)
0.837	465.750

% Hydrophobic	% Polar
55.07	44.93
According to VolSite

Ligand :

HET Code:	8IN
Formula:	C21H23N2O5P
Molecular weight:	414.391 g/mol
DrugBank ID:	DB02504
Buried Surface Area:	64.05 %
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:	9

Mass center Coordinates

X	Y	Z
59.0461	29.7962	46.8431

Binding mode :

What is Poseview ?

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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
C1	CD1	LEU- 2	3.84	0	Hydrophobic	false
C10	CE2	PHE- 5	4	0	Hydrophobic	false
C14	CE2	PHE- 5	4.45	0	Hydrophobic	false
C19	CB	HIS- 6	3.6	0	Hydrophobic	false
C21	CB	ALA- 17	3.91	0	Hydrophobic	false
C20	CB	ALA- 17	3.93	0	Hydrophobic	false
C17	CB	ALA- 18	4.13	0	Hydrophobic	false
C14	CB	TYR- 21	3.71	0	Hydrophobic	false
C14	CB	CYS- 28	4.19	0	Hydrophobic	false
O12	N	GLY- 29	2.86	122.52	H-Bond (Protein Donor)	false
C24	CG2	VAL- 30	4.45	0	Hydrophobic	false
C1	CG2	VAL- 30	3.96	0	Hydrophobic	false
O27	N	GLY- 31	3.42	147.91	H-Bond (Protein Donor)	false
O29	N	GLY- 31	2.67	144.34	H-Bond (Protein Donor)	false
C10	SG	CYS- 44	4.07	0	Hydrophobic	false
C14	SG	CYS- 44	4.4	0	Hydrophobic	false
N13	ND1	HIS- 47	2.97	170.12	H-Bond (Ligand Donor)	false
N13	OD2	ASP- 48	2.55	163.78	H-Bond (Ligand Donor)	false
C23	CD2	TYR- 51	3.69	0	Hydrophobic	false
O28	NZ	LYS- 52	3.88	0	Ionic (Protein Cationic)	false
C23	CG	LYS- 62	4.13	0	Hydrophobic	false
C14	CZ	PHE- 98	4.15	0	Hydrophobic	false
O12	CA	CA- 198	2.62	0	Metal Acceptor	false
O29	CA	CA- 198	2.38	0	Metal Acceptor	false
O28	O	HOH- 219	2.58	142.86	H-Bond (Protein Donor)	false