scPDB - 2tpl entry

Protein Data Bank Entry:

PDB ID : 2tpl

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 1997-01-23

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Tyrosine phenol-lyase
ID:	TPL_CITFR
AC:	P31013
Organism:	Citrobacter freundii
Reign:	Bacteria
TaxID:	546
EC Number:	4.1.99.2

Chains:

Chain Name:	Percentage of Residues within binding site
A	18 %
B	82 %

Ligand binding site composition:

B-Factor:	21.364
Number of residues:	22
Including
Standard Amino Acids:	21
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.153	607.500

% Hydrophobic	% Polar
47.78	52.22
According to VolSite

Ligand :

HET Code:	HPP
Formula:	C9H9O3
Molecular weight:	165.166 g/mol
DrugBank ID:	DB03897
Buried Surface Area:	50.84 %
Polar Surface area:	60.36 Å2

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

Mass center Coordinates

X	Y	Z
-23.2634	17.5466	3.92408

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
O2	OG1	THR- 49	2.5	150.09	H-Bond (Protein Donor)	false
C8	CB	SER- 51	4.29	0	Hydrophobic	false
C7	CZ	TYR- 71	3.37	0	Hydrophobic	false
C8	CZ	PHE- 123	4.28	0	Hydrophobic	false
C2	CE	MET- 379	4.41	0	Hydrophobic	false
O1	NH2	ARG- 404	3.34	139.23	H-Bond (Protein Donor)	false
O1	NH1	ARG- 404	3.03	157.47	H-Bond (Protein Donor)	false
O2	NH2	ARG- 404	3	147.37	H-Bond (Protein Donor)	false
O1	CZ	ARG- 404	3.61	0	Ionic (Protein Cationic)	false
O2	CZ	ARG- 404	3.9	0	Ionic (Protein Cationic)	false