scPDB - 3uf6 entry

Protein Data Bank Entry:

PDB ID : 3uf6

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2011-10-31

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Lmo1369 protein
ID:	Q8Y7B7_LISMO
AC:	Q8Y7B7
Organism:	Listeria monocytogenes serovar 1/2a
Reign:	Bacteria
TaxID:	169963
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	81 %
B	19 %

Ligand binding site composition:

B-Factor:	17.458
Number of residues:	33
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.958	658.125

% Hydrophobic	% Polar
46.67	53.33
According to VolSite

Ligand :

HET Code:	COD
Formula:	C21H33N7O13P2S
Molecular weight:	685.538 g/mol
DrugBank ID:	DB03170
Buried Surface Area:	62.61 %
Polar Surface area:	364.11 Å2

Number of
H-Bond Acceptors:	18
H-Bond Donors:	7
Rings:	3
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	16

Mass center Coordinates

X	Y	Z
-8.76044	39.0217	56.7485

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
C11	CB	ALA- 135	3.84	0	Hydrophobic	false
C16	CB	ALA- 135	4.18	0	Hydrophobic	false
O21	NZ	LYS- 216	3.23	120.92	H-Bond (Protein Donor)	false
O26	NZ	LYS- 216	2.94	155.27	H-Bond (Protein Donor)	false
O21	NZ	LYS- 216	3.23	0	Ionic (Protein Cationic)	false
O26	NZ	LYS- 216	2.94	0	Ionic (Protein Cationic)	false
O22	ND2	ASN- 238	2.97	165.75	H-Bond (Protein Donor)	false
O15	OH	TYR- 241	2.65	159.59	H-Bond (Ligand Donor)	false
C16	CZ	TYR- 241	3.86	0	Hydrophobic	false
O21	NZ	LYS- 242	3.01	135.88	H-Bond (Protein Donor)	false
O22	NZ	LYS- 242	2.78	130.12	H-Bond (Protein Donor)	false
O21	NZ	LYS- 242	3.01	0	Ionic (Protein Cationic)	false
O22	NZ	LYS- 242	2.78	0	Ionic (Protein Cationic)	false
O13	OG	SER- 254	3.24	138.41	H-Bond (Protein Donor)	false
O15	OG	SER- 254	2.55	125.95	H-Bond (Protein Donor)	false
O13	O	ILE- 265	2.58	171.61	H-Bond (Ligand Donor)	false
O21	OG	SER- 267	2.79	158.32	H-Bond (Protein Donor)	false
C12	CB	SER- 267	4.09	0	Hydrophobic	false
O26	O	HOH- 405	2.58	179.96	H-Bond (Protein Donor)	false