scPDB - 3lby entry

Protein Data Bank Entry:

PDB ID : 3lby

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2010-01-08

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Uncharacterized protein
ID:	Q8DSS3_STRMU
AC:	Q8DSS3
Organism:	Streptococcus mutans serotype c
Reign:	Bacteria
TaxID:	210007
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	45.120
Number of residues:	31
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.851	526.500

% Hydrophobic	% Polar
42.31	57.69
According to VolSite

Ligand :

HET Code:	SAH
Formula:	C14H20N6O5S
Molecular weight:	384.411 g/mol
DrugBank ID:	DB01752
Buried Surface Area:	70.63 %
Polar Surface area:	212.38 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
9.55335	43.4104	-5.3185

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
C4'	CB	THR- 27	4	0	Hydrophobic	false
O3'	OD1	ASP- 48	3.44	133.29	H-Bond (Ligand Donor)	false
O3'	OD2	ASP- 48	2.78	154.23	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 48	2.79	158.7	H-Bond (Ligand Donor)	false
O2'	NE2	GLN- 50	2.7	158.86	H-Bond (Protein Donor)	false
N1	N	HIS- 76	2.87	163.7	H-Bond (Protein Donor)	false
N6	OE1	GLN- 77	3.37	171.89	H-Bond (Ligand Donor)	false
CB	CB	ASN- 93	3.78	0	Hydrophobic	false
N	O	LEU- 94	3.01	154.29	H-Bond (Ligand Donor)	false
N	O	TYR- 96	2.83	171.48	H-Bond (Ligand Donor)	false
SD	CB	LEU- 97	3.91	0	Hydrophobic	false
C3'	CD2	LEU- 97	3.97	0	Hydrophobic	false
C2'	CG1	VAL- 104	4.2	0	Hydrophobic	false
C5'	CG2	THR- 106	4.4	0	Hydrophobic	false
C1'	CG2	THR- 106	4.3	0	Hydrophobic	false
CB	CE2	TYR- 133	4.29	0	Hydrophobic	false