scPDB - 4az3 entry

Protein Data Bank Entry:

PDB ID : 4az3

Resolution :2.040 Å

Experimental Method : X-ray

Deposition Date : 2012-06-22

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Lysosomal protective protein
ID:	PPGB_HUMAN
AC:	P10619
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	3.4.16.5

Chains:

Chain Name:	Percentage of Residues within binding site
A	54 %
B	46 %

Ligand binding site composition:

B-Factor:	25.079
Number of residues:	39
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.302	921.375

% Hydrophobic	% Polar
44.69	55.31
According to VolSite

Ligand :

HET Code:	S35
Formula:	C26H29FN3O5
Molecular weight:	482.524 g/mol
DrugBank ID:	-
Buried Surface Area:	57.43 %
Polar Surface area:	116.51 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	2
Rings:	3
Aromatic rings:	3
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
-34.7566	12.6262	19.1111

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
O27	ND2	ASN- 55	2.78	164.87	H-Bond (Protein Donor)	false
O27	N	GLY- 56	2.81	176.07	H-Bond (Protein Donor)	false
C29	SG	CYS- 60	4.17	0	Hydrophobic	false
C25	CB	CYS- 60	4.4	0	Hydrophobic	false
C34	CB	CYS- 60	3.58	0	Hydrophobic	false
C5	SG	CYS- 60	3.93	0	Hydrophobic	false
C33	CB	ASP- 64	3.86	0	Hydrophobic	false
O28	OE2	GLU- 149	2.82	144.81	H-Bond (Ligand Donor)	false
C25	CB	SER- 150	3.81	0	Hydrophobic	false
C35	CZ	TYR- 247	3.65	0	Hydrophobic	false
C1	CG	PRO- 301	4.22	0	Hydrophobic	false
F7	CB	PRO- 301	3.56	0	Hydrophobic	false
C35	CG	PRO- 301	3.97	0	Hydrophobic	false
C35	CG2	THR- 304	4.08	0	Hydrophobic	false
C32	CG2	THR- 306	4.29	0	Hydrophobic	false
C32	SD	MET- 333	4.07	0	Hydrophobic	false
C34	SG	CYS- 334	4.15	0	Hydrophobic	false
C4	CB	CYS- 334	3.62	0	Hydrophobic	false
C3	CB	PHE- 336	4.24	0	Hydrophobic	false
O16	ND2	ASN- 339	3.19	156.99	H-Bond (Protein Donor)	false
C4	CB	ASN- 339	3.57	0	Hydrophobic	false
C31	CE	MET- 430	4.38	0	Hydrophobic	false