scPDB - 2ay5 entry

Protein Data Bank Entry:

PDB ID : 2ay5

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 1998-08-06

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Aromatic-amino-acid aminotransferase
ID:	TYRB_PARDE
AC:	P95468
Organism:	Paracoccus denitrificans
Reign:	Bacteria
TaxID:	266
EC Number:	2.6.1.57

Chains:

Chain Name:	Percentage of Residues within binding site
A	25 %
B	75 %

Ligand binding site composition:

B-Factor:	21.911
Number of residues:	25
Including
Standard Amino Acids:	23
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.008	297.000

% Hydrophobic	% Polar
45.45	54.55
According to VolSite

Ligand :

HET Code:	IOP
Formula:	C11H10NO2
Molecular weight:	188.203 g/mol
DrugBank ID:	DB02758
Buried Surface Area:	82.57 %
Polar Surface area:	55.92 Å2

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

Mass center Coordinates

X	Y	Z
100.821	44.8658	12.2469

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
C7A	CD1	LEU- 18	4.29	0	Hydrophobic	false
C3'	CG2	VAL- 37	4.19	0	Hydrophobic	false
O2	N	GLY- 38	2.87	144.59	H-Bond (Protein Donor)	false
C3'	CE2	TYR- 70	3.51	0	Hydrophobic	false
O1	NE1	TRP- 140	2.74	134.87	H-Bond (Protein Donor)	false
O1	ND2	ASN- 194	2.97	156.68	H-Bond (Protein Donor)	false
C2'	CE	LYS- 258	4.17	0	Hydrophobic	false
C6	CB	SER- 296	3.52	0	Hydrophobic	false
O1	NH1	ARG- 386	3.24	154.21	H-Bond (Protein Donor)	false
O2	NH1	ARG- 386	3.38	139.64	H-Bond (Protein Donor)	false
O2	NH2	ARG- 386	3.15	150.21	H-Bond (Protein Donor)	false
O2	CZ	ARG- 386	3.71	0	Ionic (Protein Cationic)	false