scPDB - 3k5d entry

Protein Data Bank Entry:

PDB ID : 3k5d

Resolution :2.900 Å

Experimental Method : X-ray

Deposition Date : 2009-10-07

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:	43.098
Number of residues:	46
Including
Standard Amino Acids:	43
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.739	779.625

% Hydrophobic	% Polar
32.47	67.53
According to VolSite

Ligand :

HET Code:	XLI
Formula:	C27H52N4O5S
Molecular weight:	544.791 g/mol
DrugBank ID:	-
Buried Surface Area:	61.12 %
Polar Surface area:	161.92 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	5
Rings:	0
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	19

Mass center Coordinates

X	Y	Z
-0.909297	5.49554	33.9057

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
CD2	CD1	LEU- 30	3.68	0	Hydrophobic	false
CD11	CD2	LEU- 30	3.98	0	Hydrophobic	false
N3	O	GLY- 34	2.82	161.96	H-Bond (Ligand Donor)	false
C21	CB	SER- 35	4.03	0	Hydrophobic	false
C41	CG1	VAL- 69	3.62	0	Hydrophobic	false
C3	CD1	TYR- 71	4.09	0	Hydrophobic	false
CB2	CD1	TYR- 71	4.32	0	Hydrophobic	false
CD21	CD2	TYR- 71	3.73	0	Hydrophobic	false
SD	CG2	THR- 72	3.93	0	Hydrophobic	false
CB1	CG2	THR- 72	3.7	0	Hydrophobic	false
O4	N	THR- 72	3.09	150.25	H-Bond (Protein Donor)	false
O2	N	GLN- 73	3.01	146.92	H-Bond (Protein Donor)	false
CB1	CB	GLN- 73	3.92	0	Hydrophobic	false
CE	CG	GLN- 73	3.29	0	Hydrophobic	false
CD11	CE1	PHE- 108	3.95	0	Hydrophobic	false
CD21	CD1	PHE- 108	3.76	0	Hydrophobic	false
CB	CD1	ILE- 110	4.19	0	Hydrophobic	false
CD2	CD1	ILE- 110	4	0	Hydrophobic	false
CD2	CZ2	TRP- 115	3.94	0	Hydrophobic	false
CD11	CH2	TRP- 115	4.14	0	Hydrophobic	false
CB2	CD1	ILE- 118	4.43	0	Hydrophobic	false
CD11	CD1	ILE- 118	4.16	0	Hydrophobic	false
C21	CD1	ILE- 126	4.1	0	Hydrophobic	false
C31	CB	ILE- 126	4.41	0	Hydrophobic	false
C41	CG	ARG- 128	4.27	0	Hydrophobic	false
CB3	CE1	TYR- 198	4.22	0	Hydrophobic	false
C21	CE1	TYR- 198	4.41	0	Hydrophobic	false
CB3	CD1	ILE- 226	3.88	0	Hydrophobic	false
O3	OD2	ASP- 228	2.73	175.75	H-Bond (Ligand Donor)	false
N2	O	GLY- 230	3.29	163.17	H-Bond (Ligand Donor)	false
CH3	CB	THR- 232	3.57	0	Hydrophobic	false
N	OG1	THR- 232	2.94	129.77	H-Bond (Ligand Donor)	false
O1	N	THR- 232	2.95	144.85	H-Bond (Protein Donor)	false
CG1	CD	ARG- 235	4.1	0	Hydrophobic	false