scPDB - 2y4g entry

Protein Data Bank Entry:

PDB ID : 2y4g

Resolution :2.030 Å

Experimental Method : X-ray

Deposition Date : 2011-01-05

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	TamL
ID:	D3Y1I2_9ACTN
AC:	D3Y1I2
Organism:	Streptomyces sp. 307-9
Reign:	Bacteria
TaxID:	529089
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	17.462
Number of residues:	38
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	2
Water Molecules:	2
Cofactors:	FAD
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
1.387	1167.750

% Hydrophobic	% Polar
41.62	58.38
According to VolSite

Ligand :

HET Code:	TIR
Formula:	C22H28NO6
Molecular weight:	402.461 g/mol
DrugBank ID:	-
Buried Surface Area:	57.57 %
Polar Surface area:	107.92 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	2
Rings:	3
Aromatic rings:	0
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
11.8467	14.232	-10.7804

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
C15	CZ	TYR- 64	3.95	0	Hydrophobic	false
C21	CZ	TYR- 64	4.46	0	Hydrophobic	false
C19	CB	ALA- 121	4.32	0	Hydrophobic	false
C11	SG	CYS- 122	4.2	0	Hydrophobic	false
C19	CG2	VAL- 266	4.38	0	Hydrophobic	false
N	O	THR- 334	2.89	173.83	H-Bond (Ligand Donor)	false
C21	CG1	ILE- 339	3.6	0	Hydrophobic	false
C20	CB	ALA- 373	3.72	0	Hydrophobic	false
C19	CD1	ILE- 375	4.42	0	Hydrophobic	false
C15	CG1	VAL- 401	4.02	0	Hydrophobic	false
C9	CG1	VAL- 401	4.17	0	Hydrophobic	false
C21	CG2	VAL- 403	3.63	0	Hydrophobic	false
C9	CG2	VAL- 403	4.15	0	Hydrophobic	false
O4	OH	TYR- 447	2.53	145	H-Bond (Ligand Donor)	false
C15	CE1	TYR- 447	3.83	0	Hydrophobic	false
C16	CE1	TYR- 447	4.28	0	Hydrophobic	false
C13	C6	FAD- 600	3.38	0	Hydrophobic	false
O5	MG	MG- 900	2.13	0	Metal Acceptor	false
O6	MG	MG- 900	2.19	0	Metal Acceptor	false