scPDB - 3bcd entry

Protein Data Bank Entry:

PDB ID : 3bcd

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2007-11-12

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Alpha amylase
ID:	B8CZ54_HALOH
AC:	B8CZ54
Organism:	Halothermothrix orenii
Reign:	Bacteria
TaxID:	373903
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	11.288
Number of residues:	17
Including
Standard Amino Acids:	17
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.014	243.000

% Hydrophobic	% Polar
54.17	45.83
According to VolSite

Ligand :

HET Code:	ACX
Formula:	C36H60O30
Molecular weight:	972.844 g/mol
DrugBank ID:	DB01909
Buried Surface Area:	23.66 %
Polar Surface area:	474.9 Å2

Number of
H-Bond Acceptors:	30
H-Bond Donors:	18
Rings:	8
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
43.414	26.5332	6.24852

Binding mode :

What is Poseview ?

2D View
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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
C3D	CE	MET- 176	3.69	0	Hydrophobic	false
C3E	CE	MET- 176	3.66	0	Hydrophobic	false
O3E	NZ	LYS- 198	2.92	146.84	H-Bond (Protein Donor)	false
O2E	O	ALA- 237	2.55	154.44	H-Bond (Ligand Donor)	false
C1E	CZ3	TRP- 260	4.05	0	Hydrophobic	false
C4F	CD2	TRP- 260	3.79	0	Hydrophobic	false
C5F	CE2	TRP- 260	4.09	0	Hydrophobic	false
C6F	CZ2	TRP- 260	3.79	0	Hydrophobic	false
C3F	CB	TRP- 260	4.35	0	Hydrophobic	false
C1A	CH2	TRP- 287	4.33	0	Hydrophobic	false
C2A	CZ3	TRP- 287	3.78	0	Hydrophobic	false
C3A	CD2	TRP- 287	4.05	0	Hydrophobic	false
C4A	CE2	TRP- 287	3.71	0	Hydrophobic	false
C6A	CZ2	TRP- 287	4.15	0	Hydrophobic	false