scPDB - 3p2h entry

Protein Data Bank Entry:

PDB ID : 3p2h

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2010-10-02

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Acyl-homoserine-lactone synthase
ID:	Q4VSJ8_BURGL
AC:	Q4VSJ8
Organism:	Burkholderia glumae
Reign:	Bacteria
TaxID:	337
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	22.508
Number of residues:	23
Including
Standard Amino Acids:	20
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.321	286.875

% Hydrophobic	% Polar
63.53	36.47
According to VolSite

Ligand :

HET Code:	MTA
Formula:	C11H15N5O3S
Molecular weight:	297.333 g/mol
DrugBank ID:	DB02282
Buried Surface Area:	47.39 %
Polar Surface area:	144.61 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	3

Mass center Coordinates

X	Y	Z
3.5319	71.7054	58.5854

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
CS	CH2	TRP- 33	3.9	0	Hydrophobic	false
C4'	CE2	TRP- 33	4.38	0	Hydrophobic	false
C5'	CZ2	TRP- 33	3.46	0	Hydrophobic	false
C2'	CD2	TRP- 33	3.63	0	Hydrophobic	false
N6	OD2	ASP- 45	2.83	156.15	H-Bond (Ligand Donor)	false
N6	OE1	GLN- 46	3.03	163.67	H-Bond (Ligand Donor)	false
C4'	CZ	PHE- 83	4.08	0	Hydrophobic	false
C1'	CZ	PHE- 83	3.87	0	Hydrophobic	false
S5'	CE2	PHE- 83	4.39	0	Hydrophobic	false
N7	NH2	ARG- 104	3.24	131.8	H-Bond (Protein Donor)	false
N7	NH1	ARG- 104	3.12	135.15	H-Bond (Protein Donor)	false
S5'	CG1	VAL- 144	4.04	0	Hydrophobic	false