scPDB - 1w51 entry

Protein Data Bank Entry:

PDB ID : 1w51

Resolution :2.550 Å

Experimental Method : X-ray

Deposition Date : 2004-08-04

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:	42.294
Number of residues:	40
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.998	921.375

% Hydrophobic	% Polar
37.36	62.64
According to VolSite

Ligand :

HET Code:	L01
Formula:	C32H42N3O4
Molecular weight:	532.694 g/mol
DrugBank ID:	-
Buried Surface Area:	64.59 %
Polar Surface area:	95.48 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	3
Rings:	3
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	15

Mass center Coordinates

X	Y	Z
68.9124	47.5492	7.73713

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
C27	CD2	LEU- 30	3.69	0	Hydrophobic	false
O30	OD2	ASP- 32	2.92	166.35	H-Bond (Ligand Donor)	false
N32	O	GLY- 34	3.24	150.07	H-Bond (Ligand Donor)	false
C42	CB	SER- 35	4.3	0	Hydrophobic	false
C43	CB	SER- 35	4.31	0	Hydrophobic	false
C42	CG1	VAL- 69	4.37	0	Hydrophobic	false
C21	CD2	TYR- 71	4.38	0	Hydrophobic	false
C23	CB	TYR- 71	4.33	0	Hydrophobic	false
C28	CD2	TYR- 71	4.16	0	Hydrophobic	false
C42	CE2	TYR- 71	4.4	0	Hydrophobic	false
C37	CG2	THR- 72	3.82	0	Hydrophobic	false
C7	CG	GLN- 73	3.68	0	Hydrophobic	false
C13	CB	GLN- 73	3.5	0	Hydrophobic	false
O17	N	GLN- 73	3.27	152.36	H-Bond (Protein Donor)	false
C6	CD1	ILE- 110	4.08	0	Hydrophobic	false
C21	CD1	ILE- 118	4	0	Hydrophobic	false
N32	OD2	ASP- 228	2.76	149.8	H-Bond (Ligand Donor)	false
N32	OD2	ASP- 228	2.76	0	Ionic (Ligand Cationic)	false
N18	O	GLY- 230	2.8	157.2	H-Bond (Ligand Donor)	false
O9	OG1	THR- 232	2.76	161.32	H-Bond (Protein Donor)	false
O9	N	THR- 232	3.07	126.14	H-Bond (Protein Donor)	false