scPDB - 2ycn entry

Protein Data Bank Entry:

PDB ID : 2ycn

Resolution :2.040 Å

Experimental Method : X-ray

Deposition Date : 2011-03-16

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	14 %
B	86 %

Ligand binding site composition:

B-Factor:	29.985
Number of residues:	45
Including
Standard Amino Acids:	43
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.561	509.625

% Hydrophobic	% Polar
54.30	45.70
According to VolSite

Ligand :

HET Code:	P61
Formula:	C17H15FN2O8P
Molecular weight:	425.282 g/mol
DrugBank ID:	-
Buried Surface Area:	76.24 %
Polar Surface area:	187.21 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	3
Rings:	2
Aromatic rings:	1
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
22.924	55.3777	7.96117

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
CB	CB	SER- 51	3.93	0	Hydrophobic	false
CB	CZ	PHE- 71	3.88	0	Hydrophobic	false
O3P	NE2	GLN- 98	3.19	148.32	H-Bond (Protein Donor)	false
O2P	N	GLY- 99	2.84	150.67	H-Bond (Protein Donor)	false
O1P	NH2	ARG- 100	2.83	161.78	H-Bond (Protein Donor)	false
O3P	NE	ARG- 100	2.75	168.55	H-Bond (Protein Donor)	false
O3P	N	ARG- 100	2.79	148.64	H-Bond (Protein Donor)	false
O1P	CZ	ARG- 100	3.76	0	Ionic (Protein Cationic)	false
O3P	CZ	ARG- 100	3.58	0	Ionic (Protein Cationic)	false
CB	CZ	PHE- 123	4.38	0	Hydrophobic	false
C2A	CB	PHE- 123	4.3	0	Hydrophobic	false
C5A	CE2	PHE- 123	3.97	0	Hydrophobic	false
CE2	CG2	THR- 125	4.33	0	Hydrophobic	false
O3	ND2	ASN- 185	2.75	135.91	H-Bond (Protein Donor)	false
OXT	ND2	ASN- 185	2.83	148.21	H-Bond (Protein Donor)	false
C2A	CB	ASN- 185	4.16	0	Hydrophobic	false
N1	OD2	ASP- 214	2.65	168.83	H-Bond (Ligand Donor)	false
C2A	CB	THR- 216	4.15	0	Hydrophobic	false
O3	NH2	ARG- 217	3.38	135.48	H-Bond (Protein Donor)	false
O3	NH1	ARG- 217	2.93	158.65	H-Bond (Protein Donor)	false
OXT	NH2	ARG- 217	3.07	131.54	H-Bond (Protein Donor)	false
O2P	OG	SER- 254	2.5	147.81	H-Bond (Protein Donor)	false
O1P	NZ	LYS- 257	3.42	120.4	H-Bond (Protein Donor)	false
O4P	NZ	LYS- 257	3.42	138.43	H-Bond (Protein Donor)	false
O1P	NZ	LYS- 257	3.42	0	Ionic (Protein Cationic)	false
O2P	NZ	LYS- 257	3.66	0	Ionic (Protein Cationic)	false
CZ	CE	MET- 288	4.07	0	Hydrophobic	false
F	CE	MET- 379	3.92	0	Hydrophobic	false
CD1	CE	MET- 379	4.39	0	Hydrophobic	false
O	CZ	ARG- 404	3.44	0	Ionic (Protein Cationic)	false
OXT	CZ	ARG- 404	3.61	0	Ionic (Protein Cationic)	false
O	NH2	ARG- 404	2.65	168.19	H-Bond (Protein Donor)	false
O	NH1	ARG- 404	3.37	127.46	H-Bond (Protein Donor)	false
OXT	NH1	ARG- 404	2.77	148.69	H-Bond (Protein Donor)	false
F	CE2	PHE- 448	4.43	0	Hydrophobic	false
O1P	O	HOH- 2085	2.71	171.18	H-Bond (Protein Donor)	false
OH	O	HOH- 2414	2.68	179.96	H-Bond (Protein Donor)	false