scPDB - 4i12 entry

Protein Data Bank Entry:

PDB ID : 4i12

Resolution :1.780 Å

Experimental Method : X-ray

Deposition Date : 2012-11-19

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:	39.734
Number of residues:	40
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.451	280.125

% Hydrophobic	% Polar
43.37	56.63
According to VolSite

Ligand :

HET Code:	1BC
Formula:	C27H31ClN6OS
Molecular weight:	523.093 g/mol
DrugBank ID:	-
Buried Surface Area:	62.66 %
Polar Surface area:	126.31 Å2

Number of
H-Bond Acceptors:	3
H-Bond Donors:	4
Rings:	5
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	2
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
10.0834	-16.8523	8.15511

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
C28	CD2	LEU- 91	4.13	0	Hydrophobic	false
C27	CD2	LEU- 91	3.73	0	Hydrophobic	false
S17	CD1	LEU- 91	4.25	0	Hydrophobic	false
C20	CD1	LEU- 91	4.46	0	Hydrophobic	false
C9	CE1	TYR- 132	3.44	0	Hydrophobic	false
C2	CD1	TYR- 132	3.44	0	Hydrophobic	false
CL1	CB	TYR- 132	3.75	0	Hydrophobic	false
N25	O	LYS- 168	2.87	162.22	H-Bond (Ligand Donor)	false
CL1	CD1	PHE- 169	3.88	0	Hydrophobic	false
C27	CE1	PHE- 169	4.19	0	Hydrophobic	false
C9	CE1	PHE- 169	4.24	0	Hydrophobic	false
C2	CD1	PHE- 169	3.49	0	Hydrophobic	false
C27	CH2	TRP- 176	4.21	0	Hydrophobic	false
C28	CD1	ILE- 179	4.26	0	Hydrophobic	false
C19	CB	THR- 293	4.48	0	Hydrophobic	false
N31	N	THR- 293	3.11	175.72	H-Bond (Protein Donor)	false
O36	N	THR- 293	3.3	123.36	H-Bond (Protein Donor)	false
O36	N	ASN- 294	2.99	160.79	H-Bond (Protein Donor)	false
C21	CB	ALA- 396	3.58	0	Hydrophobic	false