scPDB - 1efa entry

Protein Data Bank Entry:

PDB ID : 1efa

Resolution :2.600 Å

Experimental Method : X-ray

Deposition Date : 2000-02-07

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Lactose operon repressor
ID:	LACI_ECOLI
AC:	P03023
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	46.040
Number of residues:	33
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.938	664.875

% Hydrophobic	% Polar
47.21	52.79
According to VolSite

Ligand :

HET Code:	NPF
Formula:	C12H15NO7
Molecular weight:	285.250 g/mol
DrugBank ID:	DB08297
Buried Surface Area:	70.44 %
Polar Surface area:	124.97 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	3
Rings:	2
Aromatic rings:	1
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	3

Mass center Coordinates

X	Y	Z
43.907	80.9215	60.4431

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
C1	CB	ALA- 75	3.89	0	Hydrophobic	false
C1'	CB	ALA- 75	4.11	0	Hydrophobic	false
C6'	CD1	ILE- 79	4.19	0	Hydrophobic	false
O3'	O	LEU- 148	3.16	158.38	H-Bond (Ligand Donor)	false
O2'	OD2	ASP- 149	3.38	155.58	H-Bond (Ligand Donor)	false
C6'	CD1	PHE- 161	3.56	0	Hydrophobic	false
C3'	CB	SER- 193	3.66	0	Hydrophobic	false
O6A	NH1	ARG- 197	3.39	157.67	H-Bond (Protein Donor)	false
C1	CE2	TRP- 220	4.03	0	Hydrophobic	false
O6B	ND2	ASN- 246	2.97	157	H-Bond (Protein Donor)	false
O6B	OD2	ASP- 274	2.84	123.59	H-Bond (Ligand Donor)	false
C6'	CE2	PHE- 293	3.28	0	Hydrophobic	false
C6'	CD2	LEU- 296	4.15	0	Hydrophobic	false