scPDB - 3c1o entry

Protein Data Bank Entry:

PDB ID : 3c1o

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2008-01-23

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Eugenol synthase
ID:	D0VWT0_CLABR
AC:	D0VWT0
Organism:	Clarkia breweri
Reign:	Eukaryota
TaxID:	36903
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	18.300
Number of residues:	49
Including
Standard Amino Acids:	47
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.323	793.125

% Hydrophobic	% Polar
59.15	40.85
According to VolSite

Ligand :

HET Code:	NAP
Formula:	C21H25N7O17P3
Molecular weight:	740.381 g/mol
DrugBank ID:	DB03461
Buried Surface Area:	56.7 %
Polar Surface area:	405.54 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	5
Rings:	5
Aromatic rings:	3
Anionic atoms:	4
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
55.9737	-2.69267	14.1875

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
O3B	OG1	THR- 10	2.63	165.83	H-Bond (Ligand Donor)	false
O1X	OG1	THR- 10	2.58	160.51	H-Bond (Protein Donor)	false
O2A	N	TYR- 12	2.72	173.48	H-Bond (Protein Donor)	false
O2N	N	ILE- 13	3.12	172.3	H-Bond (Protein Donor)	false
C5D	CG2	ILE- 13	4.09	0	Hydrophobic	false
O2X	NE	ARG- 33	2.83	173.75	H-Bond (Protein Donor)	false
O3X	NH2	ARG- 33	2.89	164.81	H-Bond (Protein Donor)	false
O2X	CZ	ARG- 33	3.7	0	Ionic (Protein Cationic)	false
O3X	CZ	ARG- 33	3.75	0	Ionic (Protein Cationic)	false
DuAr	CZ	ARG- 33	3.78	159.46	Pi/Cation	false
O1X	NH1	ARG- 47	2.93	167.64	H-Bond (Protein Donor)	false
O2X	NH2	ARG- 47	2.73	153.68	H-Bond (Protein Donor)	false
O1X	CZ	ARG- 47	3.79	0	Ionic (Protein Cationic)	false
O2X	CZ	ARG- 47	3.54	0	Ionic (Protein Cationic)	false
C5B	CG	PRO- 83	3.72	0	Hydrophobic	false
O3D	OG	SER- 109	2.71	166.83	H-Bond (Ligand Donor)	false
N7N	O	PHE- 111	3	153.99	H-Bond (Ligand Donor)	false
O3D	NZ	LYS- 131	2.93	126.89	H-Bond (Protein Donor)	false
O2D	NZ	LYS- 131	2.83	148.22	H-Bond (Protein Donor)	false
N7N	O	ASN- 151	2.78	145.25	H-Bond (Ligand Donor)	false
O7N	N	PHE- 153	2.91	173.64	H-Bond (Protein Donor)	false
DuAr	DuAr	PHE- 153	3.82	0	Aromatic Face/Face	false
C4N	CB	PHE- 153	4.35	0	Hydrophobic	false
O2N	O	HOH- 1001	2.72	179.96	H-Bond (Protein Donor)	false