scPDB - 2p4j entry

Protein Data Bank Entry:

PDB ID : 2p4j

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2007-03-12

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	8.960	8.960	8.960	0.000	8.960	1

List of CHEMBLId :

CHEMBL387771

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:	33.060
Number of residues:	52
Including
Standard Amino Acids:	50
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.758	759.375

% Hydrophobic	% Polar
34.22	65.78
According to VolSite

Ligand :

HET Code:	23I
Formula:	C36H55N5O7S
Molecular weight:	701.916 g/mol
DrugBank ID:	-
Buried Surface Area:	64.71 %
Polar Surface area:	182.38 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	5
Rings:	2
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	17

Mass center Coordinates

X	Y	Z
-3.27027	-3.38435	30.9899

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
C35	CD2	LEU- 30	3.34	0	Hydrophobic	false
C18	CD1	LEU- 30	4.18	0	Hydrophobic	false
O31	OD2	ASP- 32	3.45	143.95	H-Bond (Ligand Donor)	false
N4	O	GLY- 34	3.24	168.74	H-Bond (Ligand Donor)	false
C42	CB	SER- 35	3.78	0	Hydrophobic	false
C43	CG1	VAL- 69	4.11	0	Hydrophobic	false
N5	O	PRO- 70	2.71	174.25	H-Bond (Ligand Donor)	false
C53	CG	PRO- 70	3.83	0	Hydrophobic	false
C32	CD1	TYR- 71	3.84	0	Hydrophobic	false
C33	CD1	TYR- 71	3.66	0	Hydrophobic	false
C36	CG	TYR- 71	3.99	0	Hydrophobic	false
C26	CB	THR- 72	4.26	0	Hydrophobic	false
C29	CG2	THR- 72	4.01	0	Hydrophobic	false
O32	N	THR- 72	3.01	152.02	H-Bond (Protein Donor)	false
O22	N	GLN- 73	2.99	135.01	H-Bond (Protein Donor)	false
C26	CB	GLN- 73	3.75	0	Hydrophobic	false
C35	CE1	PHE- 108	3.98	0	Hydrophobic	false
C36	CD1	PHE- 108	3.76	0	Hydrophobic	false
C18	CD1	ILE- 110	3.54	0	Hydrophobic	false
C35	CH2	TRP- 115	4.05	0	Hydrophobic	false
C18	CZ2	TRP- 115	4.5	0	Hydrophobic	false
C33	CD1	ILE- 118	4.11	0	Hydrophobic	false
C35	CD1	ILE- 118	4.06	0	Hydrophobic	false
C44	CD1	ILE- 126	3.68	0	Hydrophobic	false
C44	CE1	TYR- 198	3.65	0	Hydrophobic	false
C39	CD1	ILE- 226	3.91	0	Hydrophobic	false
O31	OD2	ASP- 228	2.61	167.15	H-Bond (Protein Donor)	false
N21	O	GLY- 230	3.08	170.79	H-Bond (Ligand Donor)	false
N3	O	GLY- 230	3.49	166.12	H-Bond (Ligand Donor)	false
C25	CG2	THR- 231	4.49	0	Hydrophobic	false
C12	CG2	THR- 232	4.26	0	Hydrophobic	false
C24	CB	THR- 232	4.41	0	Hydrophobic	false
C11	CB	THR- 232	4.35	0	Hydrophobic	false
O24	N	ASN- 233	2.8	162.45	H-Bond (Protein Donor)	false
C29	CD	ARG- 235	3.34	0	Hydrophobic	false
C13	CB	ALA- 335	3.52	0	Hydrophobic	false