scPDB - 4lrl entry

Protein Data Bank Entry:

PDB ID : 4lrl

Resolution :2.350 Å

Experimental Method : X-ray

Deposition Date : 2013-07-19

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	HD domain protein
ID:	Q836G9_ENTFA
AC:	Q836G9
Organism:	Enterococcus faecalis
Reign:	Bacteria
TaxID:	226185
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
B	4 %
C	48 %
D	48 %

Ligand binding site composition:

B-Factor:	34.883
Number of residues:	24
Including
Standard Amino Acids:	23
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.347	2278.125

% Hydrophobic	% Polar
37.48	62.52
According to VolSite

Ligand :

HET Code:	DGT
Formula:	C10H12N5O13P3
Molecular weight:	503.149 g/mol
DrugBank ID:	DB02181
Buried Surface Area:	54.13 %
Polar Surface area:	315.33 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	3
Rings:	3
Aromatic rings:	1
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
-3.89694	-1.18265	17.5091

Binding mode :

What is Poseview ?

2D View
3D View

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
O1G	NZ	LYS- 14	3.36	166.49	H-Bond (Protein Donor)	false
O2A	NZ	LYS- 14	2.52	170.6	H-Bond (Protein Donor)	false
O3'	NZ	LYS- 14	3.18	146.32	H-Bond (Protein Donor)	false
O1G	NZ	LYS- 14	3.36	0	Ionic (Protein Cationic)	false
O3G	NZ	LYS- 14	3.12	0	Ionic (Protein Cationic)	false
O2B	NZ	LYS- 14	2.77	0	Ionic (Protein Cationic)	false
O2A	NZ	LYS- 14	2.52	0	Ionic (Protein Cationic)	false
C3'	CD	LYS- 14	4.1	0	Hydrophobic	false
C2'	CD2	PHE- 16	3.76	0	Hydrophobic	false
N1	OD1	ASN- 36	3.06	149.49	H-Bond (Ligand Donor)	false
N2	OD1	ASN- 36	2.99	151.12	H-Bond (Ligand Donor)	false
O6	NE2	GLN- 41	2.91	154.61	H-Bond (Protein Donor)	false
N7	NH2	ARG- 44	2.87	132.47	H-Bond (Protein Donor)	false
O6	NH2	ARG- 44	2.72	150.52	H-Bond (Protein Donor)	false
C4'	CG2	THR- 55	4.45	0	Hydrophobic	false
C5'	CG2	VAL- 247	3.84	0	Hydrophobic	false
O1A	NH2	ARG- 326	2.69	167.42	H-Bond (Protein Donor)	false
O1A	NH1	ARG- 326	3.33	130.69	H-Bond (Protein Donor)	false
O5'	NH1	ARG- 326	2.95	157.78	H-Bond (Protein Donor)	false
O1A	CZ	ARG- 326	3.45	0	Ionic (Protein Cationic)	false
O1B	NZ	LYS- 330	2.7	122.86	H-Bond (Protein Donor)	false
O1B	NZ	LYS- 330	2.7	0	Ionic (Protein Cationic)	false
O2G	NZ	LYS- 422	3.26	167.41	H-Bond (Protein Donor)	false
O2G	NZ	LYS- 422	3.26	0	Ionic (Protein Cationic)	false
O3G	NZ	LYS- 422	3.72	0	Ionic (Protein Cationic)	false