scPDB - 3lnv entry

Protein Data Bank Entry:

PDB ID : 3lnv

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2010-02-03

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Saframycin Mx1 synthetase B
ID:	Q5ZTD3_LEGPH
AC:	Q5ZTD3
Organism:	Legionella pneumophila subsp. pneumophila
Reign:	Bacteria
TaxID:	272624
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	17.962
Number of residues:	47
Including
Standard Amino Acids:	45
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.246	2497.500

% Hydrophobic	% Polar
45.14	54.86
According to VolSite

Ligand :

HET Code:	1ZZ
Formula:	C22H35N5O8P
Molecular weight:	528.516 g/mol
DrugBank ID:	-
Buried Surface Area:	70.32 %
Polar Surface area:	204.77 Å2

Number of
H-Bond Acceptors:	12
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	16

Mass center Coordinates

X	Y	Z
19.1846	33.7151	34.8146

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
O4	N	SER- 174	3.46	131.83	H-Bond (Protein Donor)	false
C1	CG2	ILE- 197	3.7	0	Hydrophobic	false
C3	CZ	PHE- 201	3.81	0	Hydrophobic	false
C5	CZ	PHE- 201	4.3	0	Hydrophobic	false
C2	CE2	PHE- 201	3.43	0	Hydrophobic	false
C1	CE	MET- 203	3.4	0	Hydrophobic	false
C11	CB	ASP- 218	4.24	0	Hydrophobic	false
C4	CB	MET- 219	3.95	0	Hydrophobic	false
C5	CG	MET- 219	4.43	0	Hydrophobic	false
C8	CG	MET- 219	4.29	0	Hydrophobic	false
C9	SD	MET- 219	3.46	0	Hydrophobic	false
C6	SD	MET- 219	3.69	0	Hydrophobic	false
C11	CG	MET- 219	4.38	0	Hydrophobic	false
C2	CE2	PHE- 293	3.65	0	Hydrophobic	false
C4	CE1	PHE- 293	4.1	0	Hydrophobic	false
N2	N	ALA- 296	3.17	142.21	H-Bond (Protein Donor)	false
C10	CB	ALA- 296	3.93	0	Hydrophobic	false
N5	O	CYS- 324	2.93	147.37	H-Bond (Ligand Donor)	false
C7	SG	CYS- 324	3.53	0	Hydrophobic	false
C6	SG	CYS- 324	3.47	0	Hydrophobic	false
C15	CE1	TYR- 325	4.33	0	Hydrophobic	false
C13	CB	LEU- 327	3.72	0	Hydrophobic	false
C15	CB	LEU- 327	4.38	0	Hydrophobic	false
O3	N	ALA- 328	3.25	174.96	H-Bond (Protein Donor)	false
C7	CG	LEU- 332	4.38	0	Hydrophobic	false
C11	CD1	LEU- 332	4	0	Hydrophobic	false
C8	CD1	LEU- 332	4.08	0	Hydrophobic	false
C5	CD2	LEU- 332	3.55	0	Hydrophobic	false
C7	CD1	LEU- 333	3.59	0	Hydrophobic	false
C5	CD1	LEU- 333	4.08	0	Hydrophobic	false
N5	OG	SER- 374	3.15	131.75	H-Bond (Ligand Donor)	false
O7	OD1	ASP- 440	2.96	159.86	H-Bond (Ligand Donor)	false