scPDB - 4i0h entry

Protein Data Bank Entry:

PDB ID : 4i0h

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2012-11-16

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Beta-secretase 1
ID:	BACE1_HUMAN
AC:	P56817
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	3.4.23.46

Chains:

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

Ligand binding site composition:

B-Factor:	59.671
Number of residues:	45
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.161	985.500

% Hydrophobic	% Polar
36.30	63.70
According to VolSite

Ligand :

HET Code:	1BL
Formula:	C31H42F2N2O5
Molecular weight:	560.672 g/mol
DrugBank ID:	-
Buried Surface Area:	61.14 %
Polar Surface area:	126.3 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
-23.4713	-41.9322	-1.1293

Binding mode :

What is Poseview ?

2D View
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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
F7	CD1	LEU- 36	3.45	0	Hydrophobic	false
O40	OD1	ASP- 38	2.74	155.22	H-Bond (Ligand Donor)	false
O40	OD2	ASP- 38	3.39	145.33	H-Bond (Ligand Donor)	false
N13	O	GLY- 40	3.23	157.64	H-Bond (Ligand Donor)	false
C39	CB	SER- 41	3.58	0	Hydrophobic	false
C39	CG1	VAL- 75	3.77	0	Hydrophobic	false
C37	CG1	VAL- 75	4.41	0	Hydrophobic	false
C11	CD1	TYR- 77	4.1	0	Hydrophobic	false
C9	CD1	TYR- 77	3.88	0	Hydrophobic	false
F8	CD2	TYR- 77	4.11	0	Hydrophobic	false
C39	CE1	TYR- 77	3.8	0	Hydrophobic	false
C4	CB	TYR- 77	3.83	0	Hydrophobic	false
O24	N	THR- 78	3.15	158.29	H-Bond (Protein Donor)	false
C18	CB	THR- 78	4.13	0	Hydrophobic	false
F8	CD1	PHE- 114	3.21	0	Hydrophobic	false
F7	CD1	ILE- 116	3.94	0	Hydrophobic	false
F7	CZ2	TRP- 121	3.53	0	Hydrophobic	false
C9	CD1	ILE- 124	3.98	0	Hydrophobic	false
C38	CD1	ILE- 132	4.05	0	Hydrophobic	false
C38	CE1	TYR- 204	4.2	0	Hydrophobic	false
C26	CE1	TYR- 204	3.46	0	Hydrophobic	false
C26	CD1	ILE- 232	3.77	0	Hydrophobic	false
N13	OD2	ASP- 234	2.77	164.24	H-Bond (Ligand Donor)	false
N13	OD2	ASP- 234	2.77	0	Ionic (Ligand Cationic)	false
N16	O	GLY- 236	3.03	162.72	H-Bond (Ligand Donor)	false
O23	N	THR- 238	3.12	145.61	H-Bond (Protein Donor)	false
O23	OG1	THR- 238	2.87	158.56	H-Bond (Protein Donor)	false
O22	N	THR- 238	3.47	159.74	H-Bond (Protein Donor)	false
C28	CG2	THR- 335	3.67	0	Hydrophobic	false
C27	CG2	VAL- 338	3.58	0	Hydrophobic	false