scPDB - 3ies entry

Protein Data Bank Entry:

PDB ID : 3ies

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2009-07-23

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Luciferin 4-monooxygenase
ID:	LUCI_PHOPY
AC:	P08659
Organism:	Photinus pyralis
Reign:	Eukaryota
TaxID:	7054
EC Number:	1.13.12.7

Chains:

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

Ligand binding site composition:

B-Factor:	22.365
Number of residues:	51
Including
Standard Amino Acids:	45
Non Standard Amino Acids:	0
Water Molecules:	6
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.561	351.000

% Hydrophobic	% Polar
45.19	54.81
According to VolSite

Ligand :

HET Code:	M24
Formula:	C25H20FN7O9P
Molecular weight:	612.440 g/mol
DrugBank ID:	-
Buried Surface Area:	67.43 %
Polar Surface area:	243.69 Å2

Number of
H-Bond Acceptors:	14
H-Bond Donors:	3
Rings:	6
Aromatic rings:	5
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
-29.8411	6.79267	-10.8917

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
O1P	NE2	HIS- 245	2.8	169.33	H-Bond (Protein Donor)	false
DuAr	DuAr	PHE- 247	3.91	0	Aromatic Face/Face	false
C30	CB	PHE- 247	3.91	0	Hydrophobic	false
C42	CG2	THR- 251	3.85	0	Hydrophobic	false
C39	CB	ALA- 313	3.94	0	Hydrophobic	false
N7	N	GLY- 316	3.05	140.26	H-Bond (Protein Donor)	false
N6	OE1	GLN- 338	3.36	145.24	H-Bond (Ligand Donor)	false
N6	O	GLY- 339	2.77	148.31	H-Bond (Ligand Donor)	false
C2'	CE2	TYR- 340	3.84	0	Hydrophobic	false
C3'	CD2	LEU- 342	3.93	0	Hydrophobic	false
C5'	CB	LEU- 342	3.97	0	Hydrophobic	false
O3P	N	THR- 343	2.93	162.41	H-Bond (Protein Donor)	false
O3P	OG1	THR- 343	2.78	157.84	H-Bond (Protein Donor)	false
F43	CB	ALA- 348	3.48	0	Hydrophobic	false
C41	CD1	ILE- 351	4.37	0	Hydrophobic	false
O2'	OD1	ASP- 422	2.7	167.1	H-Bond (Ligand Donor)	false
O3'	OD1	ASP- 422	3.38	121.04	H-Bond (Ligand Donor)	false
O3'	OD2	ASP- 422	2.84	162.63	H-Bond (Ligand Donor)	false
O3P	O	HOH- 778	3.03	179.94	H-Bond (Protein Donor)	false