scPDB - 3l7l entry

Protein Data Bank Entry:

PDB ID : 3l7l

Resolution :2.950 Å

Experimental Method : X-ray

Deposition Date : 2009-12-28

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Teichoic acid poly(glycerol phosphate) polymerase
ID:	Q5HLM5_STAEQ
AC:	Q5HLM5
Organism:	Staphylococcus epidermidis
Reign:	Bacteria
TaxID:	176279
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	90.974
Number of residues:	35
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.772	945.000

% Hydrophobic	% Polar
39.64	60.36
According to VolSite

Ligand :

HET Code:	C2G
Formula:	C12H19N3O13P2
Molecular weight:	475.239 g/mol
DrugBank ID:	DB02484
Buried Surface Area:	56.41 %
Polar Surface area:	276.4 Å2

Number of
H-Bond Acceptors:	15
H-Bond Donors:	5
Rings:	2
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
-71.4016	78.2347	6.14603

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	NE1	TRP- 443	2.77	129.27	H-Bond (Protein Donor)	false
O2G	OD1	ASN- 444	2.64	128.79	H-Bond (Ligand Donor)	false
C1G	CB	PRO- 447	3.98	0	Hydrophobic	false
N4	O	PRO- 545	3.12	163.84	H-Bond (Ligand Donor)	false
O1A	OG1	THR- 546	2.88	124.75	H-Bond (Protein Donor)	false
O2	NH2	ARG- 582	3.44	133.6	H-Bond (Protein Donor)	false
O2	NE	ARG- 582	2.85	173.75	H-Bond (Protein Donor)	false
N4	O	ARG- 582	3.13	163.54	H-Bond (Ligand Donor)	false
C2'	CG1	VAL- 609	4.47	0	Hydrophobic	false
O1A	OG	SER- 624	3.1	164.32	H-Bond (Protein Donor)	false
O5'	OG	SER- 625	3.26	168.68	H-Bond (Protein Donor)	false
O2A	N	SER- 625	2.97	158.41	H-Bond (Protein Donor)	false
C1G	CB	SER- 625	4.08	0	Hydrophobic	false
C3G	CB	SER- 625	3.94	0	Hydrophobic	false
C2'	CG1	VAL- 626	3.6	0	Hydrophobic	false
O3'	OD1	ASP- 629	2.92	147.77	H-Bond (Ligand Donor)	false