scPDB - 3rix entry

Protein Data Bank Entry:

PDB ID : 3rix

Resolution :1.700 Å

Experimental Method : X-ray

Deposition Date : 2011-04-14

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:	25.611
Number of residues:	45
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.564	324.000

% Hydrophobic	% Polar
52.08	47.92
According to VolSite

Ligand :

HET Code:	923
Formula:	C27H27O7
Molecular weight:	463.499 g/mol
DrugBank ID:	-
Buried Surface Area:	65.69 %
Polar Surface area:	108.28 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	2
Rings:	5
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
-28.4175	3.96632	-9.01121

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
O30	NH2	ARG- 218	2.95	160.7	H-Bond (Protein Donor)	false
O27	NE2	HIS- 245	2.8	160.33	H-Bond (Protein Donor)	false
C10	CE1	PHE- 247	3.77	0	Hydrophobic	false
C16	CB	PHE- 247	4.29	0	Hydrophobic	false
C7	CG2	THR- 251	4.46	0	Hydrophobic	false
C31	CG2	THR- 251	4.15	0	Hydrophobic	false
C31	CZ	TYR- 255	4.45	0	Hydrophobic	false
C4	CB	ALA- 313	3.81	0	Hydrophobic	false
O27	O	GLY- 316	2.98	155.7	H-Bond (Ligand Donor)	false
O34	N	GLY- 316	2.73	165.49	H-Bond (Protein Donor)	false
C4	CG	ARG- 337	4.49	0	Hydrophobic	false
O24	OG1	THR- 343	3	150.95	H-Bond (Protein Donor)	false
O33	OG	SER- 347	2.85	142.61	H-Bond (Ligand Donor)	false
C1	CB	ALA- 348	3.45	0	Hydrophobic	false
C1	CB	ALA- 348	3.45	0	Hydrophobic	false
C5	CG2	ILE- 351	4.39	0	Hydrophobic	false
C7	CD1	ILE- 351	4.15	0	Hydrophobic	false
C8	CG2	ILE- 351	4.2	0	Hydrophobic	false
O30	O	HOH- 611	2.69	160.29	H-Bond (Ligand Donor)	false
O30	O	HOH- 615	2.74	179.98	H-Bond (Protein Donor)	false