scPDB - 1lqa entry

Protein Data Bank Entry:

PDB ID : 1lqa

Resolution :1.600 Å

Experimental Method : X-ray

Deposition Date : 2002-05-09

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Protein tas
ID:	TAS_ECOLI
AC:	P0A9T4
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	12.279
Number of residues:	57
Including
Standard Amino Acids:	54
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.039	982.125

% Hydrophobic	% Polar
47.77	52.23
According to VolSite

Ligand :

HET Code:	NDP
Formula:	C21H26N7O17P3
Molecular weight:	741.389 g/mol
DrugBank ID:	DB02338
Buried Surface Area:	77.98 %
Polar Surface area:	404.9 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	5
Rings:	5
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
22.1449	44.451	25.0255

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
C3D	CG	MET- 21	3.64	0	Hydrophobic	false
C2D	SD	MET- 21	4.1	0	Hydrophobic	false
C5N	SD	MET- 21	3.9	0	Hydrophobic	false
O3D	N	MET- 21	3.13	170.56	H-Bond (Protein Donor)	false
O1X	NE2	GLN- 26	2.93	161.94	H-Bond (Protein Donor)	false
O2D	OD2	ASP- 48	2.67	161.27	H-Bond (Ligand Donor)	false
C2D	CE2	TYR- 53	4.08	0	Hydrophobic	false
N7N	OG	SER- 179	2.81	138.71	H-Bond (Ligand Donor)	false
O7N	ND2	ASN- 180	2.96	170.53	H-Bond (Protein Donor)	false
N7N	OE1	GLN- 205	3.03	176.96	H-Bond (Ligand Donor)	false
C3N	CB	TYR- 233	4.32	0	Hydrophobic	false
C5N	CB	TYR- 233	4.45	0	Hydrophobic	false
DuAr	DuAr	TYR- 233	3.57	0	Aromatic Face/Face	false
O2N	OG	SER- 234	2.7	170.59	H-Bond (Protein Donor)	false
O1A	N	LEU- 236	3.34	137.71	H-Bond (Protein Donor)	false
O2A	N	LEU- 236	3.07	133.25	H-Bond (Protein Donor)	false
O2A	N	PHE- 238	2.79	141.62	H-Bond (Protein Donor)	false
N3A	NZ	LYS- 244	2.94	143.1	H-Bond (Protein Donor)	false
O2X	NZ	LYS- 244	2.62	147.29	H-Bond (Protein Donor)	false
O2X	NZ	LYS- 244	2.62	0	Ionic (Protein Cationic)	false
O3X	NZ	LYS- 244	3.71	0	Ionic (Protein Cationic)	false
O3B	NH2	ARG- 255	3.2	120.73	H-Bond (Protein Donor)	false
O1N	NH2	ARG- 255	2.72	171.59	H-Bond (Protein Donor)	false
O2N	NH1	ARG- 255	3.1	170.25	H-Bond (Protein Donor)	false
O1X	N	ARG- 255	2.77	128.26	H-Bond (Protein Donor)	false
O1N	CZ	ARG- 255	3.6	0	Ionic (Protein Cationic)	false
O2N	CZ	ARG- 255	3.98	0	Ionic (Protein Cationic)	false
C4D	CB	LEU- 306	4.14	0	Hydrophobic	false
O3X	OG1	THR- 310	2.69	149.94	H-Bond (Protein Donor)	false
C2B	CG2	THR- 310	4.25	0	Hydrophobic	false
O3X	NE2	GLN- 314	2.95	175.81	H-Bond (Protein Donor)	false
N7A	ND2	ASN- 318	2.84	164.5	H-Bond (Protein Donor)	false
N6A	OD1	ASN- 318	2.96	169.36	H-Bond (Ligand Donor)	false
O1A	O	HOH- 1443	2.83	179.97	H-Bond (Protein Donor)	false