scPDB - 3u9e entry

Protein Data Bank Entry:

PDB ID : 3u9e

Resolution :2.040 Å

Experimental Method : X-ray

Deposition Date : 2011-10-18

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	19 %
B	81 %

Ligand binding site composition:

B-Factor:	38.936
Number of residues:	30
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.869	877.500

% Hydrophobic	% Polar
40.00	60.00
According to VolSite

Ligand :

HET Code:	COA
Formula:	C21H32N7O16P3S
Molecular weight:	763.502 g/mol
DrugBank ID:	DB01992
Buried Surface Area:	49.9 %
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
-18.5205	3.02255	-2.06077

Binding mode :

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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
O5A	NZ	LYS- 89	3.82	0	Ionic (Protein Cationic)	false
C2B	CB	THR- 94	4.29	0	Hydrophobic	false
O5A	N	THR- 94	3.38	146.92	H-Bond (Protein Donor)	false
C2B	CG2	ILE- 265	4.41	0	Hydrophobic	false
O9A	OG	SER- 267	2.67	141.23	H-Bond (Protein Donor)	false
O7A	CZ	ARG- 268	3.72	0	Ionic (Protein Cationic)	false
O8A	CZ	ARG- 268	3.62	0	Ionic (Protein Cationic)	false
O6A	CZ	ARG- 268	3.82	0	Ionic (Protein Cationic)	false
O7A	N	ARG- 268	2.97	166.57	H-Bond (Protein Donor)	false
O7A	NE	ARG- 268	2.9	171.5	H-Bond (Protein Donor)	false
O8A	NH2	ARG- 268	2.7	170.66	H-Bond (Protein Donor)	false
O7A	O	HOH- 323	3.23	158.6	H-Bond (Protein Donor)	false