scPDB - 4gid entry

Protein Data Bank Entry:

PDB ID : 4gid

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2012-08-08

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	7.010	7.010	7.010	0.000	7.010	1

List of CHEMBLId :

CHEMBL2179132

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
C	100 %

Ligand binding site composition:

B-Factor:	23.550
Number of residues:	55
Including
Standard Amino Acids:	51
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.980	918.000

% Hydrophobic	% Polar
32.72	67.28
According to VolSite

Ligand :

HET Code:	0GH
Formula:	C35H48N5O6S
Molecular weight:	666.851 g/mol
DrugBank ID:	-
Buried Surface Area:	70.83 %
Polar Surface area:	169.89 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	5
Rings:	3
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	16

Mass center Coordinates

X	Y	Z
3.02396	43.8149	11.4279

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
CBS	CD1	LEU- 78	4.09	0	Hydrophobic	false
CBA	CD2	LEU- 78	3.41	0	Hydrophobic	false
CBM	CB	SER- 83	3.42	0	Hydrophobic	false
CBK	CG1	VAL- 117	4.17	0	Hydrophobic	false
CAY	CD1	TYR- 119	3.87	0	Hydrophobic	false
CBE	CB	TYR- 119	3.9	0	Hydrophobic	false
OBV	N	THR- 120	3.12	152.83	H-Bond (Protein Donor)	false
CBJ	CB	THR- 120	3.6	0	Hydrophobic	false
CBT	CG2	THR- 120	3.86	0	Hydrophobic	false
OAU	N	GLN- 121	3.28	134	H-Bond (Protein Donor)	false
OAM	NE2	GLN- 121	2.96	135.42	H-Bond (Protein Donor)	false
CAO	CB	GLN- 121	3.84	0	Hydrophobic	false
CBS	CD1	ILE- 158	3.52	0	Hydrophobic	false
CBS	CZ2	TRP- 163	4.15	0	Hydrophobic	false
CBA	CD1	ILE- 166	3.65	0	Hydrophobic	false
CBM	CD1	ILE- 174	3.81	0	Hydrophobic	false
CBM	CE1	TYR- 246	3.93	0	Hydrophobic	false
CBH	CD1	ILE- 274	4.05	0	Hydrophobic	false
NBF	OD1	ASP- 276	3.88	0	Ionic (Ligand Cationic)	false
NBF	OD2	ASP- 276	2.63	0	Ionic (Ligand Cationic)	false
NBF	OD2	ASP- 276	2.63	155.1	H-Bond (Ligand Donor)	false
NAV	O	GLY- 278	3.08	167.45	H-Bond (Ligand Donor)	false
NBQ	O	GLY- 278	3.02	171.55	H-Bond (Ligand Donor)	false
NBF	OG1	THR- 279	3.49	136.82	H-Bond (Ligand Donor)	false
CAP	CB	THR- 279	4.19	0	Hydrophobic	false
CAN	CG2	THR- 279	4.01	0	Hydrophobic	false
CAS	CB	THR- 280	4.45	0	Hydrophobic	false
CAG	CG2	THR- 280	4.07	0	Hydrophobic	false
CAH	CB	THR- 280	4.07	0	Hydrophobic	false
OAD	N	ASN- 281	2.98	178.75	H-Bond (Protein Donor)	false
CBT	CD	ARG- 283	3.55	0	Hydrophobic	false
CAF	CB	ALA- 383	3.47	0	Hydrophobic	false