scPDB - 3lbe entry

Protein Data Bank Entry:

PDB ID : 3lbe

Resolution :1.700 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:	Q8DUV0_STRMU
AC:	Q8DUV0
Organism:	Streptococcus mutans serotype c
Reign:	Bacteria
TaxID:	210007
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	41 %
B	32 %
C	26 %

Ligand binding site composition:

B-Factor:	30.750
Number of residues:	36
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:	COA
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.833	600.750

% Hydrophobic	% Polar
44.38	55.62
According to VolSite

Ligand :

HET Code:	COA
Formula:	C21H32N7O16P3S
Molecular weight:	763.502 g/mol
DrugBank ID:	DB01992
Buried Surface Area:	47.41 %
Polar Surface area:	426.11 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	6
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	18

Mass center Coordinates

X	Y	Z
68.0645	44.0978	18.8992

Binding mode :

What is Poseview ?

2D View
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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
C2P	CB	PHE- 41	4.17	0	Hydrophobic	false
S1P	CD2	PHE- 41	4.46	0	Hydrophobic	false
CDP	CG2	VAL- 67	4.1	0	Hydrophobic	false
CEP	CG2	VAL- 67	4.28	0	Hydrophobic	false
C6P	CG2	VAL- 67	4.01	0	Hydrophobic	false
S1P	CB	VAL- 67	3.73	0	Hydrophobic	false
N4P	O	THR- 68	2.91	164.75	H-Bond (Ligand Donor)	false
CCP	CD1	LEU- 69	4.49	0	Hydrophobic	false
CDP	CD1	LEU- 69	3.53	0	Hydrophobic	false
N8P	O	TYR- 75	2.84	147.54	H-Bond (Ligand Donor)	false
C6P	CB	TYR- 75	3.74	0	Hydrophobic	false
O5P	OG	SER- 78	2.84	156.18	H-Bond (Protein Donor)	false
O3A	NE2	HIS- 93	3.18	128.51	H-Bond (Protein Donor)	false
O5A	NE2	HIS- 93	2.97	162.05	H-Bond (Protein Donor)	false
O2B	NH2	ARG- 96	3.44	168.12	H-Bond (Protein Donor)	false
O1A	N	ARG- 96	2.84	167.86	H-Bond (Protein Donor)	false
N6A	OG1	THR- 97	2.97	162.42	H-Bond (Ligand Donor)	false
N7A	OG1	THR- 97	2.59	168.99	H-Bond (Protein Donor)	false
O4A	N	THR- 97	2.79	162.71	H-Bond (Protein Donor)	false
O5A	N	THR- 98	3.07	137.16	H-Bond (Protein Donor)	false
O5A	OG1	THR- 98	2.55	152	H-Bond (Protein Donor)	false
CCP	CE1	PHE- 121	4.21	0	Hydrophobic	false
CDP	CB	PHE- 121	3.96	0	Hydrophobic	false
CEP	CD2	PHE- 121	3.87	0	Hydrophobic	false
O2A	O	HOH- 143	2.65	149.7	H-Bond (Protein Donor)	false
O5P	O	HOH- 144	2.76	159.33	H-Bond (Protein Donor)	false