scPDB - 3lst entry

Protein Data Bank Entry:

PDB ID : 3lst

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 2010-02-12

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	CalO1
ID:	Q8KNE5_MICEC
AC:	Q8KNE5
Organism:	Micromonospora echinospora
Reign:	Bacteria
TaxID:	1877
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	97 %
B	3 %

Ligand binding site composition:

B-Factor:	47.659
Number of residues:	33
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.320	759.375

% Hydrophobic	% Polar
45.33	54.67
According to VolSite

Ligand :

HET Code:	SAH
Formula:	C14H20N6O5S
Molecular weight:	384.411 g/mol
DrugBank ID:	DB01752
Buried Surface Area:	63.38 %
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
33.6501	67.5163	101.829

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
SD	CE	MET- 162	4.5	0	Hydrophobic	false
O	OG	SER- 166	2.9	152.93	H-Bond (Protein Donor)	false
N	O	GLY- 189	3	167.89	H-Bond (Ligand Donor)	false
O3'	OD2	ASP- 212	3.16	174.22	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 212	2.7	173.2	H-Bond (Ligand Donor)	false
N6	OD1	ASP- 237	2.76	171.66	H-Bond (Ligand Donor)	false
C1'	CE2	PHE- 238	4.28	0	Hydrophobic	false
N1	N	PHE- 238	3.05	149.65	H-Bond (Protein Donor)	false
DuAr	DuAr	PHE- 238	3.36	0	Aromatic Face/Face	false
N	O	LYS- 251	3.06	146.04	H-Bond (Ligand Donor)	false
O	NZ	LYS- 251	3.91	0	Ionic (Protein Cationic)	false
OXT	NZ	LYS- 251	2.73	0	Ionic (Protein Cationic)	false
OXT	NZ	LYS- 251	2.73	147.9	H-Bond (Protein Donor)	false
CB	CB	ARG- 252	3.96	0	Hydrophobic	false
CB	CD1	ILE- 253	4.27	0	Hydrophobic	false
C5'	CD1	ILE- 253	3.48	0	Hydrophobic	false
N	O	HOH- 359	2.65	150.46	H-Bond (Ligand Donor)	false