scPDB - 3i25 entry

Protein Data Bank Entry:

PDB ID : 3i25

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2009-06-29

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	8.510	8.510	8.510	0.000	8.510	1

List of CHEMBLId :

CHEMBL591644

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:	33.234
Number of residues:	64
Including
Standard Amino Acids:	59
Non Standard Amino Acids:	0
Water Molecules:	5
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.680	438.750

% Hydrophobic	% Polar
40.00	60.00
According to VolSite

Ligand :

HET Code:	MV7
Formula:	C45H55F2N5O10S
Molecular weight:	896.008 g/mol
DrugBank ID:	-
Buried Surface Area:	68.67 %
Polar Surface area:	210.07 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	5
Rings:	4
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	23

Mass center Coordinates

X	Y	Z
-0.324429	17.0554	33.9672

Binding mode :

What is Poseview ?

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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
C39	CD1	LEU- 30	3.72	0	Hydrophobic	false
C27	CD2	LEU- 30	3.89	0	Hydrophobic	false
C21	CB	ASP- 32	4.28	0	Hydrophobic	false
O5	OD2	ASP- 32	3.41	144.99	H-Bond (Ligand Donor)	false
N2	O	GLY- 34	3.05	170.63	H-Bond (Ligand Donor)	false
C11	CB	SER- 35	3.82	0	Hydrophobic	false
C12	CG1	VAL- 69	3.34	0	Hydrophobic	false
N1	O	PRO- 70	2.97	168.67	H-Bond (Ligand Donor)	false
C3	CG	PRO- 70	4.4	0	Hydrophobic	false
C8	CB	PRO- 70	3.62	0	Hydrophobic	false
C21	CD1	TYR- 71	3.96	0	Hydrophobic	false
F1	CD2	TYR- 71	3.37	0	Hydrophobic	false
C19	CD1	TYR- 71	3.91	0	Hydrophobic	false
C12	CE1	TYR- 71	4.12	0	Hydrophobic	false
C23	CB	TYR- 71	3.82	0	Hydrophobic	false
C32	CG2	THR- 72	3.49	0	Hydrophobic	false
C30	CB	THR- 72	4.18	0	Hydrophobic	false
O2	N	THR- 72	3.22	133.74	H-Bond (Protein Donor)	false
O10	NE2	GLN- 73	3.46	135.2	H-Bond (Protein Donor)	false
O7	N	GLN- 73	3.16	136.66	H-Bond (Protein Donor)	false
F1	CB	GLN- 73	3.91	0	Hydrophobic	false
C29	CB	GLN- 73	3.74	0	Hydrophobic	false
F1	CD1	PHE- 108	3.47	0	Hydrophobic	false
C39	CD1	ILE- 110	3.94	0	Hydrophobic	false
F2	CD1	ILE- 110	3.32	0	Hydrophobic	false
C39	CZ2	TRP- 115	4.2	0	Hydrophobic	false
F2	CZ2	TRP- 115	3.77	0	Hydrophobic	false
C21	CD1	ILE- 118	3.84	0	Hydrophobic	false
C22	CD1	ILE- 118	4.45	0	Hydrophobic	false
C11	CD1	ILE- 126	3.55	0	Hydrophobic	false
C15	CE1	TYR- 198	3.79	0	Hydrophobic	false
C11	CE1	TYR- 198	3.8	0	Hydrophobic	false
C15	CD1	ILE- 226	3.72	0	Hydrophobic	false
O5	OD2	ASP- 228	2.58	151.56	H-Bond (Protein Donor)	false
N5	O	GLY- 230	3.13	154.92	H-Bond (Ligand Donor)	false
N3	O	GLY- 230	3.23	170.9	H-Bond (Ligand Donor)	false
C29	CB	THR- 231	4.36	0	Hydrophobic	false
C31	CG2	THR- 231	4.17	0	Hydrophobic	false
C43	CB	THR- 232	4.21	0	Hydrophobic	false
C44	CG2	THR- 232	3.88	0	Hydrophobic	false
O8	N	ASN- 233	3.02	141.42	H-Bond (Protein Donor)	false
C32	CD	ARG- 235	4.05	0	Hydrophobic	false
C17	CB	THR- 329	3.81	0	Hydrophobic	false
C16	CG2	VAL- 332	3.73	0	Hydrophobic	false
C45	CB	ALA- 335	3.58	0	Hydrophobic	false