scPDB - 1n08 entry

Protein Data Bank Entry:

PDB ID : 1n08

Resolution :1.600 Å

Experimental Method : X-ray

Deposition Date : 2002-10-11

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Riboflavin kinase
ID:	RIFK_SCHPO
AC:	O74866
Organism:	Schizosaccharomyces pombe
Reign:	Eukaryota
TaxID:	284812
EC Number:	2.7.1.26

Chains:

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

Ligand binding site composition:

B-Factor:	23.989
Number of residues:	31
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.033	357.750

% Hydrophobic	% Polar
42.45	57.55
According to VolSite

Ligand :

HET Code:	ADP
Formula:	C10H12N5O10P2
Molecular weight:	424.177 g/mol
DrugBank ID:	-
Buried Surface Area:	73.89 %
Polar Surface area:	260.7 Å2

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

Mass center Coordinates

X	Y	Z
-0.760222	0.872481	-12.7137

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
O2B	N	GLY- 33	2.72	163.33	H-Bond (Protein Donor)	false
O1A	OG	SER- 38	2.91	156.15	H-Bond (Protein Donor)	false
O1A	N	SER- 38	3	133.31	H-Bond (Protein Donor)	false
O2A	N	LYS- 39	3.17	150.28	H-Bond (Protein Donor)	false
O4'	NZ	LYS- 39	2.85	131.33	H-Bond (Protein Donor)	false
C5'	CB	PRO- 44	4.5	0	Hydrophobic	false
C1'	CB	PRO- 44	4.41	0	Hydrophobic	false
C3'	CB	ALA- 46	4.19	0	Hydrophobic	false
N6	O	LEU- 99	2.77	158.52	H-Bond (Ligand Donor)	false
N1	N	LEU- 99	2.94	170.74	H-Bond (Protein Donor)	false
C1'	CB	ASP- 106	4.31	0	Hydrophobic	false
C2'	CZ	PHE- 107	3.73	0	Hydrophobic	false
C1'	CE2	PHE- 107	4.24	0	Hydrophobic	false
O2'	N	PHE- 107	2.98	166.79	H-Bond (Protein Donor)	false
O2B	OH	TYR- 108	3.23	159.39	H-Bond (Protein Donor)	false
C4'	CZ	TYR- 108	3.98	0	Hydrophobic	false
O1B	ZN	ZN- 501	2.15	0	Metal Acceptor	false
O1A	ZN	ZN- 501	2.72	0	Metal Acceptor	false