scPDB - 1ee0 entry

Protein Data Bank Entry:

PDB ID : 1ee0

Resolution :2.050 Å

Experimental Method : X-ray

Deposition Date : 2000-01-28

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	2-pyrone synthase
ID:	2PS_GERHY
AC:	P48391
Organism:	Gerbera hybrida
Reign:	Eukaryota
TaxID:	18101
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	2 %
B	98 %

Ligand binding site composition:

B-Factor:	23.979
Number of residues:	47
Including
Standard Amino Acids:	46
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.250	762.750

% Hydrophobic	% Polar
60.62	39.38
According to VolSite

Ligand :

HET Code:	CAA
Formula:	C25H36N7O18P3S
Molecular weight:	847.576 g/mol
DrugBank ID:	DB03059
Buried Surface Area:	60.67 %
Polar Surface area:	446.75 Å2

Number of
H-Bond Acceptors:	23
H-Bond Donors:	5
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	22

Mass center Coordinates

X	Y	Z
-13.6006	27.8018	65.4985

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
O3B	NZ	LYS- 60	3.23	158.17	H-Bond (Protein Donor)	false
O7A	CZ	ARG- 63	3.79	0	Ionic (Protein Cationic)	false
O8A	CZ	ARG- 63	3.3	0	Ionic (Protein Cationic)	false
O7A	NH2	ARG- 63	2.83	169.41	H-Bond (Protein Donor)	false
O8A	NH2	ARG- 63	3.31	122.99	H-Bond (Protein Donor)	false
C4B	CG1	ILE- 64	3.51	0	Hydrophobic	false
CCP	CB	LYS- 67	3.77	0	Hydrophobic	false
CDP	CB	LYS- 67	4.12	0	Hydrophobic	false
CDP	CG2	THR- 68	4.32	0	Hydrophobic	false
C4	CG2	THR- 137	4.33	0	Hydrophobic	false
C4	CE	MET- 142	4.39	0	Hydrophobic	false
O3	N	CSD- 169	3.13	155.91	H-Bond (Protein Donor)	false
C1B	CG2	VAL- 215	4.44	0	Hydrophobic	false
CEP	CG1	VAL- 215	3.77	0	Hydrophobic	false
CEP	CD2	LEU- 219	4.37	0	Hydrophobic	false
C2P	CD1	LEU- 219	4.49	0	Hydrophobic	false
C2P	CZ	PHE- 220	4.02	0	Hydrophobic	false
S1P	SD	MET- 259	3.58	0	Hydrophobic	false
C2	SD	MET- 259	3.85	0	Hydrophobic	false
C2	CD1	LEU- 261	3.64	0	Hydrophobic	false
C4	CD2	LEU- 261	3.56	0	Hydrophobic	false
N6A	O	LEU- 272	2.84	155.06	H-Bond (Ligand Donor)	false
C2P	CD2	LEU- 272	3.93	0	Hydrophobic	false
C2B	CD	ARG- 274	4.45	0	Hydrophobic	false
O2A	CZ	ARG- 274	3.96	0	Ionic (Protein Cationic)	false
O2A	NH2	ARG- 274	2.97	158.5	H-Bond (Protein Donor)	false
N4P	O	GLY- 310	2.84	170.98	H-Bond (Ligand Donor)	false
O4A	NH1	ARG- 312	3.18	143.34	H-Bond (Protein Donor)	false
O4A	NH2	ARG- 312	2.96	155.92	H-Bond (Protein Donor)	false
O6A	NH1	ARG- 312	3.37	148.93	H-Bond (Protein Donor)	false
O4A	CZ	ARG- 312	3.54	0	Ionic (Protein Cationic)	false
CAP	CB	ALA- 313	3.75	0	Hydrophobic	false
O9P	N	ALA- 313	3.38	155.5	H-Bond (Protein Donor)	false
C6P	CD1	ILE- 314	3.96	0	Hydrophobic	false
C4	CG2	ILE- 343	4.38	0	Hydrophobic	false
C2	CG	PRO- 380	4.07	0	Hydrophobic	false