scPDB - 2fdp entry

Protein Data Bank Entry:

PDB ID : 2fdp

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2005-12-14

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	7.590	7.590	7.590	0.000	7.590	1

List of CHEMBLId :

CHEMBL200077

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
B	100 %

Ligand binding site composition:

B-Factor:	16.648
Number of residues:	43
Including
Standard Amino Acids:	40
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.843	921.375

% Hydrophobic	% Polar
32.97	67.03
According to VolSite

Ligand :

HET Code:	FRP
Formula:	C33H42FN4O3
Molecular weight:	561.710 g/mol
DrugBank ID:	-
Buried Surface Area:	66.31 %
Polar Surface area:	106.15 Å2

Number of
H-Bond Acceptors:	3
H-Bond Donors:	3
Rings:	3
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	14

Mass center Coordinates

X	Y	Z
-15.6539	-5.27193	19.0751

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
C31	CD2	LEU- 30	3.87	0	Hydrophobic	false
C30	CD1	LEU- 30	4.02	0	Hydrophobic	false
C14	CD1	LEU- 30	4.36	0	Hydrophobic	false
N4	OD1	ASP- 32	2.86	160.81	H-Bond (Ligand Donor)	false
N4	OD1	ASP- 32	2.86	0	Ionic (Ligand Cationic)	false
N4	OD2	ASP- 32	3.55	0	Ionic (Ligand Cationic)	false
N3	O	GLY- 34	2.98	157.29	H-Bond (Ligand Donor)	false
C25	CB	SER- 35	3.72	0	Hydrophobic	false
C22	CG1	VAL- 69	3.88	0	Hydrophobic	false
C17	CD1	TYR- 71	3.7	0	Hydrophobic	false
C33	CB	TYR- 71	3.85	0	Hydrophobic	false
C6	CB	THR- 72	4.08	0	Hydrophobic	false
O3	N	THR- 72	3.31	140.45	H-Bond (Protein Donor)	false
O2	N	GLN- 73	3.01	175.02	H-Bond (Protein Donor)	false
C6	CB	GLN- 73	3.67	0	Hydrophobic	false
C28	CD1	PHE- 108	3.5	0	Hydrophobic	false
C11	CD1	ILE- 110	4.2	0	Hydrophobic	false
C10	CD1	ILE- 110	3.84	0	Hydrophobic	false
C32	CD1	ILE- 118	3.86	0	Hydrophobic	false
C25	CD1	ILE- 126	3.84	0	Hydrophobic	false
F1	CG	ARG- 128	3.36	0	Hydrophobic	false
C21	CE1	TYR- 198	4.24	0	Hydrophobic	false
C21	CD1	ILE- 226	3.96	0	Hydrophobic	false
N4	OD2	ASP- 228	2.61	157.26	H-Bond (Ligand Donor)	false
N4	OD2	ASP- 228	2.61	0	Ionic (Ligand Cationic)	false
N4	OD1	ASP- 228	2.82	0	Ionic (Ligand Cationic)	false
N4	O	GLY- 230	3.29	160.26	H-Bond (Ligand Donor)	false
N2	O	GLY- 230	3.08	164.4	H-Bond (Ligand Donor)	false
C2	CG2	THR- 231	4.14	0	Hydrophobic	false
O1	OG1	THR- 232	2.81	150.35	H-Bond (Protein Donor)	false
O1	N	THR- 232	2.76	150.94	H-Bond (Protein Donor)	false