scPDB - 3e4a entry

Protein Data Bank Entry:

PDB ID : 3e4a

Resolution :2.600 Å

Experimental Method : X-ray

Deposition Date : 2008-08-11

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Insulin-degrading enzyme
ID:	IDE_HUMAN
AC:	P14735
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	3.4.24.56

Chains:

Chain Name:	Percentage of Residues within binding site
B	100 %

Ligand binding site composition:

B-Factor:	33.880
Number of residues:	33
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.797	887.625

% Hydrophobic	% Polar
35.74	64.26
According to VolSite

Ligand :

HET Code:	QIX
Formula:	C25H35N8O6
Molecular weight:	543.595 g/mol
DrugBank ID:	-
Buried Surface Area:	45.49 %
Polar Surface area:	243.35 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	9
Rings:	2
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	16

Mass center Coordinates

X	Y	Z
-46.9305	85.6521	57.2272

Binding mode :

What is Poseview ?

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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
N16	OE1	GLN- 111	2.97	137.94	H-Bond (Ligand Donor)	false
O17	NE2	GLN- 111	3.3	148.74	H-Bond (Protein Donor)	false
C28	CB	HIS- 112	4.35	0	Hydrophobic	false
C18	CE1	PHE- 115	4.35	0	Hydrophobic	false
C27	CB	PHE- 115	3.84	0	Hydrophobic	false
C24	CD2	LEU- 116	3.57	0	Hydrophobic	false
C25	CD2	LEU- 116	3.69	0	Hydrophobic	false
N09	OD1	ASN- 139	2.84	163.93	H-Bond (Ligand Donor)	false
C06	CE1	PHE- 820	3.74	0	Hydrophobic	false
C05	CZ	PHE- 820	4.32	0	Hydrophobic	false
O11	NH2	ARG- 824	3.1	132.4	H-Bond (Protein Donor)	false
O11	NH1	ARG- 824	2.79	146.42	H-Bond (Protein Donor)	false
C12	CE1	TYR- 831	4.49	0	Hydrophobic	false
O15	OH	TYR- 831	2.74	136.74	H-Bond (Protein Donor)	false
O17	ZN	ZN- 2000	2.12	0	Metal Acceptor	false
O15	ZN	ZN- 2000	2.31	0	Metal Acceptor	false