scPDB - 3vdc entry

Protein Data Bank Entry:

PDB ID : 3vdc

Resolution :2.550 Å

Experimental Method : X-ray

Deposition Date : 2012-01-04

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Beta-galactosidase
ID:	BGAL_ECOLI
AC:	P00722
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	3.2.1.23

Chains:

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

Ligand binding site composition:

B-Factor:	42.827
Number of residues:	25
Including
Standard Amino Acids:	23
Non Standard Amino Acids:	2
Water Molecules:	0
Cofactors:
Metals:	MG NA

Cavity properties

Ligandability	Volume (Å3)
0.243	627.750

% Hydrophobic	% Polar
45.16	54.84
According to VolSite

Ligand :

HET Code:	IPT
Formula:	C9H18O5S
Molecular weight:	238.301 g/mol
DrugBank ID:	DB01862
Buried Surface Area:	62.02 %
Polar Surface area:	115.45 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	4
Rings:	1
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	3

Mass center Coordinates

X	Y	Z
11.9813	23.0507	23.4245

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
O5	ND2	ASN- 102	2.99	170.49	H-Bond (Protein Donor)	false
C1'	CG2	VAL- 103	4.17	0	Hydrophobic	false
O2	OE2	GLU- 461	2.68	162.81	H-Bond (Ligand Donor)	false
C3	CE2	TYR- 503	3.97	0	Hydrophobic	false
O3	OE1	GLU- 537	2.79	179.12	H-Bond (Ligand Donor)	false
O6	NE2	HIS- 540	2.81	169.81	H-Bond (Ligand Donor)	false
C6	CD1	PHE- 601	3.79	0	Hydrophobic	false
C3'	CD2	TRP- 999	3.48	0	Hydrophobic	false
C5	CZ3	TRP- 999	3.54	0	Hydrophobic	false
C1	CH2	TRP- 999	3.69	0	Hydrophobic	false