scPDB - 2d1t entry

Protein Data Bank Entry:

PDB ID : 2d1t

Resolution :1.450 Å

Experimental Method : X-ray

Deposition Date : 2005-08-31

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_LUCCR
AC:	P13129
Organism:	Luciola cruciata
Reign:	Eukaryota
TaxID:	7051
EC Number:	1.13.12.7

Chains:

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

Ligand binding site composition:

B-Factor:	6.026
Number of residues:	50
Including
Standard Amino Acids:	45
Non Standard Amino Acids:	1
Water Molecules:	4
Cofactors:
Metals:	CL

Cavity properties

Ligandability	Volume (Å3)
1.220	1201.500

% Hydrophobic	% Polar
38.76	61.24
According to VolSite

Ligand :

HET Code:	SLU
Formula:	C21H17N8O8S3
Molecular weight:	605.603 g/mol
DrugBank ID:	-
Buried Surface Area:	74.74 %
Polar Surface area:	304.71 Å2

Number of
H-Bond Acceptors:	14
H-Bond Donors:	4
Rings:	6
Aromatic rings:	5
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
18.9118	25.3727	9.5161

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
O19	N	SER- 201	3.26	164.09	H-Bond (Protein Donor)	false
O19	NE2	HIS- 247	2.84	146.59	H-Bond (Protein Donor)	false
S12	CB	PHE- 249	4.31	0	Hydrophobic	false
S9	CD1	PHE- 249	3.7	0	Hydrophobic	false
C4	CE1	PHE- 249	3.35	0	Hydrophobic	false
C2	CG2	THR- 253	3.46	0	Hydrophobic	false
C6	CD1	ILE- 288	3.95	0	Hydrophobic	false
N37	N	GLY- 318	3.11	132.05	H-Bond (Protein Donor)	false
N38	OE1	GLN- 340	3.28	147.79	H-Bond (Ligand Donor)	false
N38	O	GLY- 341	2.84	155.28	H-Bond (Ligand Donor)	false
C24	CE1	TYR- 342	3.83	0	Hydrophobic	false
C21	CG	LEU- 344	3.93	0	Hydrophobic	false
C23	CG	LEU- 344	4.07	0	Hydrophobic	false
O18	N	THR- 345	3.14	167.82	H-Bond (Protein Donor)	false
O18	OG1	THR- 345	2.95	157.38	H-Bond (Protein Donor)	false
C4	CB	ALA- 350	3.96	0	Hydrophobic	false
C2	CB	ALA- 350	3.77	0	Hydrophobic	false
O27	OD2	ASP- 424	2.6	154.71	H-Bond (Ligand Donor)	false
O27	OD1	ASP- 424	3.21	142.44	H-Bond (Ligand Donor)	false
O28	OD1	ASP- 424	2.68	164.7	H-Bond (Ligand Donor)	false
O19	NZ	LYS- 531	3.39	127.49	H-Bond (Protein Donor)	false
C22	CD	LYS- 531	3.84	0	Hydrophobic	false
C25	CD	LYS- 531	3.77	0	Hydrophobic	false
O39	O	HOH- 2007	2.68	163.73	H-Bond (Protein Donor)	false