scPDB - 2vnm entry

Protein Data Bank Entry:

PDB ID : 2vnm

Resolution :1.790 Å

Experimental Method : X-ray

Deposition Date : 2008-02-05

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:	14.757
Number of residues:	47
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	0
Water Molecules:	5
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.479	330.750

% Hydrophobic	% Polar
40.82	59.18
According to VolSite

Ligand :

HET Code:	CM8
Formula:	C31H38F3N4O4S
Molecular weight:	619.718 g/mol
DrugBank ID:	-
Buried Surface Area:	67.71 %
Polar Surface area:	123.73 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	4
Rings:	4
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
30.0193	1.96479	34.4587

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
C26	CD1	LEU- 91	3.55	0	Hydrophobic	false
O31	OD1	ASP- 93	3.48	134.69	H-Bond (Ligand Donor)	false
O31	OD2	ASP- 93	2.54	169.24	H-Bond (Ligand Donor)	false
N33	O	GLY- 95	2.99	144.74	H-Bond (Ligand Donor)	false
C40	CB	SER- 96	4.39	0	Hydrophobic	false
F42	CB	SER- 96	4.09	0	Hydrophobic	false
F43	CG1	VAL- 130	3.83	0	Hydrophobic	false
C23	CD1	TYR- 132	3.93	0	Hydrophobic	false
C29	CB	TYR- 132	4.04	0	Hydrophobic	false
C30	CD1	TYR- 132	4.08	0	Hydrophobic	false
C41	CD1	TYR- 132	4.36	0	Hydrophobic	false
F43	CE1	TYR- 132	3.38	0	Hydrophobic	false
C12	CG2	THR- 133	3.91	0	Hydrophobic	false
C14	CB	THR- 133	4.04	0	Hydrophobic	false
C12	CB	GLN- 134	4.49	0	Hydrophobic	false
C15	CB	GLN- 134	3.79	0	Hydrophobic	false
O20	N	GLN- 134	3.03	160.35	H-Bond (Protein Donor)	false
C01	CD1	ILE- 171	4.1	0	Hydrophobic	false
C27	CD1	ILE- 171	4.35	0	Hydrophobic	false
C23	CD1	ILE- 179	3.62	0	Hydrophobic	false
F42	CD1	ILE- 187	3.79	0	Hydrophobic	false
F42	CE1	TYR- 259	4.2	0	Hydrophobic	false
N33	OD1	ASP- 289	3.84	0	Ionic (Ligand Cationic)	false
N33	OD2	ASP- 289	2.6	0	Ionic (Ligand Cationic)	false
N33	OD2	ASP- 289	2.6	163.21	H-Bond (Ligand Donor)	false
N21	O	GLY- 291	2.84	175.05	H-Bond (Ligand Donor)	false
C15	CB	THR- 292	4.44	0	Hydrophobic	false
C14	CG2	THR- 292	4.1	0	Hydrophobic	false
C18	CB	THR- 293	4.29	0	Hydrophobic	false
O09	N	ASN- 294	2.96	149.72	H-Bond (Protein Donor)	false