scPDB - 3c8b entry

Protein Data Bank Entry:

PDB ID : 3c8b

Resolution :1.470 Å

Experimental Method : X-ray

Deposition Date : 2008-02-11

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Botulinum neurotoxin type A
ID:	BXA1_CLOBO
AC:	P10845
Organism:	Clostridium botulinum
Reign:	Bacteria
TaxID:	1491
EC Number:	3.4.24.69

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	18.715
Number of residues:	35
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	1
Water Molecules:	4
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.450	610.875

% Hydrophobic	% Polar
34.25	65.75
According to VolSite

Ligand :

HET Code:	ARG_ARG_GLY_ILE_NH2
Formula:	C20H43N10O4
Molecular weight:	487.620 g/mol
DrugBank ID:	-
Buried Surface Area:	51.69 %
Polar Surface area:	264.02 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	10
Rings:	0
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	3
Rule of Five Violation:	2
Rotatable Bonds:	17

Mass center Coordinates

X	Y	Z
26.6349	22.4221	55.3869

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
NE	O	ILE- 161	3.2	176.46	H-Bond (Ligand Donor)	false
CD	CD2	PHE- 163	3.99	0	Hydrophobic	false
NE	OE1	GLU- 164	2.92	130.68	H-Bond (Ligand Donor)	false
NH2	OE1	GLU- 164	3.11	124.82	H-Bond (Ligand Donor)	false
CZ	OE1	GLU- 164	3.38	0	Ionic (Ligand Cationic)	false
CG	CB	GLU- 164	3.63	0	Hydrophobic	false
CD	CZ	PHE- 194	3.6	0	Hydrophobic	false
CD	CG2	THR- 220	4.34	0	Hydrophobic	false
CD1	CZ	TYR- 251	3.82	0	Hydrophobic	false
CD1	CD1	LEU- 256	3.44	0	Hydrophobic	false
O	NH1	ARG- 363	2.95	151.11	H-Bond (Protein Donor)	false
O	OH	TYR- 366	2.76	162.56	H-Bond (Protein Donor)	false
CD1	CE1	PHE- 369	3.82	0	Hydrophobic	false
CZ	OD1	ASP- 370	3.33	0	Ionic (Ligand Cationic)	false
NH1	OD1	ASP- 370	2.91	140.74	H-Bond (Ligand Donor)	false
NH2	OD1	ASP- 370	2.92	140.34	H-Bond (Ligand Donor)	false
O	N	ASP- 370	2.73	160.33	H-Bond (Protein Donor)	false
CB	CE2	PHE- 423	4.36	0	Hydrophobic	false
O	ZN	ZN- 450	2.3	0	Metal Acceptor	false
N	O	HOH- 491	3.14	132.72	H-Bond (Ligand Donor)	false
N	O	HOH- 537	2.94	164.45	H-Bond (Ligand Donor)	false