scPDB - 3cid entry

Protein Data Bank Entry:

PDB ID : 3cid

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2008-03-11

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
B	100 %

Ligand binding site composition:

B-Factor:	17.829
Number of residues:	50
Including
Standard Amino Acids:	45
Non Standard Amino Acids:	0
Water Molecules:	5
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.950	880.875

% Hydrophobic	% Polar
35.63	64.37
According to VolSite

Ligand :

HET Code:	318
Formula:	C34H41F2N4O4
Molecular weight:	607.711 g/mol
DrugBank ID:	-
Buried Surface Area:	65.03 %
Polar Surface area:	106.56 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	3
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
19.6429	32.695	57.2089

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
C20	CD2	LEU- 91	3.66	0	Hydrophobic	false
O1	OD2	ASP- 93	2.73	163.25	H-Bond (Ligand Donor)	false
N2	O	GLY- 95	3.19	123.69	H-Bond (Ligand Donor)	false
C13	CB	SER- 96	3.8	0	Hydrophobic	false
C12	CG1	VAL- 130	3.94	0	Hydrophobic	false
F2	CD2	TYR- 132	4.1	0	Hydrophobic	false
C2	CD1	TYR- 132	4.31	0	Hydrophobic	false
C6	CD1	TYR- 132	3.85	0	Hydrophobic	false
C16	CB	TYR- 132	3.66	0	Hydrophobic	false
O2	N	THR- 133	2.99	163.47	H-Bond (Protein Donor)	false
C26	CB	THR- 133	3.82	0	Hydrophobic	false
C27	CG2	THR- 133	4.15	0	Hydrophobic	false
F2	CG	GLN- 134	3.59	0	Hydrophobic	false
C18	CG	GLN- 134	4.06	0	Hydrophobic	false
C17	CB	GLN- 134	3.85	0	Hydrophobic	false
C33	CG	GLN- 134	3.54	0	Hydrophobic	false
C21	CB	GLN- 134	3.31	0	Hydrophobic	false
O3	N	GLN- 134	2.89	152.18	H-Bond (Protein Donor)	false
F2	CD1	PHE- 169	3.38	0	Hydrophobic	false
F1	CD1	ILE- 171	3.66	0	Hydrophobic	false
C30	CD1	ILE- 171	3.78	0	Hydrophobic	false
C33	CD1	ILE- 171	3.77	0	Hydrophobic	false
F1	CZ2	TRP- 176	3.44	0	Hydrophobic	false
C6	CD1	ILE- 179	4.16	0	Hydrophobic	false
C14	CD1	ILE- 187	4.43	0	Hydrophobic	false
N2	OD1	ASP- 289	3.62	0	Ionic (Ligand Cationic)	false
N1	O	GLY- 291	3	161.1	H-Bond (Ligand Donor)	false
C22	CB	THR- 292	4.4	0	Hydrophobic	false
C23	CG2	THR- 292	4.35	0	Hydrophobic	false
O4	N	THR- 293	2.75	156.16	H-Bond (Protein Donor)	false
C27	CD	ARG- 296	4.37	0	Hydrophobic	false