scPDB - 3rvi entry

Protein Data Bank Entry:

PDB ID : 3rvi

Resolution :2.650 Å

Experimental Method : X-ray

Deposition Date : 2011-05-06

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
A	100 %

Ligand binding site composition:

B-Factor:	27.590
Number of residues:	37
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.812	759.375

% Hydrophobic	% Polar
44.44	55.56
According to VolSite

Ligand :

HET Code:	RVI
Formula:	C29H37N3O
Molecular weight:	443.624 g/mol
DrugBank ID:	-
Buried Surface Area:	60.78 %
Polar Surface area:	68 Å2

Number of
H-Bond Acceptors:	3
H-Bond Donors:	2
Rings:	4
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
66.9995	48.9232	10.604

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
N13	OD2	ASP- 32	2.65	166.15	H-Bond (Ligand Donor)	false
N18	OD1	ASP- 32	2.86	168.56	H-Bond (Ligand Donor)	false
N18	OD2	ASP- 32	3.41	127.88	H-Bond (Ligand Donor)	false
N22	O	GLY- 34	3.22	167.26	H-Bond (Ligand Donor)	false
C26	CB	SER- 35	3.54	0	Hydrophobic	false
C27	CG1	VAL- 69	4.12	0	Hydrophobic	false
C10	CB	TYR- 71	4.43	0	Hydrophobic	false
C17	CD2	TYR- 71	3.73	0	Hydrophobic	false
C29	CD1	TYR- 71	3.84	0	Hydrophobic	false
C2	CB	TYR- 71	3.8	0	Hydrophobic	false
C1	CB	PHE- 108	4.12	0	Hydrophobic	false
C9	CD1	ILE- 118	3.46	0	Hydrophobic	false
C26	CD	ARG- 128	4.19	0	Hydrophobic	false
C32	CE1	TYR- 198	3.6	0	Hydrophobic	false
C32	CD1	ILE- 226	3.65	0	Hydrophobic	false
N18	OD2	ASP- 228	2.9	148.7	H-Bond (Ligand Donor)	false
C33	CB	THR- 329	3.76	0	Hydrophobic	false
C31	CG2	VAL- 332	4.39	0	Hydrophobic	false
C33	CG2	VAL- 332	3.69	0	Hydrophobic	false