scPDB - 1n07 entry

Protein Data Bank Entry:

PDB ID : 1n07

Resolution :2.450 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:	41.597
Number of residues:	34
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:	ADP
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.494	772.875

% Hydrophobic	% Polar
44.54	55.46
According to VolSite

Ligand :

HET Code:	FMN
Formula:	C17H19N4O9P
Molecular weight:	454.328 g/mol
DrugBank ID:	DB03247
Buried Surface Area:	60.05 %
Polar Surface area:	217.05 Å2

Number of
H-Bond Acceptors:	12
H-Bond Donors:	4
Rings:	3
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
7.18768	8.30752	-5.60871

Binding mode :

What is Poseview ?

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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
O3P	N	PHE- 34	3.02	133.36	H-Bond (Protein Donor)	false
O3'	NH1	ARG- 36	3.25	132.3	H-Bond (Protein Donor)	false
C8M	CG2	THR- 45	3.71	0	Hydrophobic	false
C6	CG2	VAL- 64	3.45	0	Hydrophobic	false
C7M	CG1	VAL- 64	3.61	0	Hydrophobic	false
C7M	CG2	VAL- 79	3.81	0	Hydrophobic	false
C7	CB	SER- 81	3.67	0	Hydrophobic	false
C8	CB	SER- 81	3.62	0	Hydrophobic	false
C8	CB	SER- 81	3.62	0	Hydrophobic	false
O4	NH1	ARG- 121	3.36	133.81	H-Bond (Protein Donor)	false
O4	NH2	ARG- 121	2.85	161.05	H-Bond (Protein Donor)	false
N5	NH1	ARG- 121	3.3	145.19	H-Bond (Protein Donor)	false
N3	O	LEU- 124	2.75	166.51	H-Bond (Ligand Donor)	false
O4	N	LEU- 124	2.9	152.7	H-Bond (Protein Donor)	false
C9A	CD1	LEU- 132	3.86	0	Hydrophobic	false
C1'	CD2	LEU- 132	3.65	0	Hydrophobic	false
C7M	CG2	ILE- 136	4.33	0	Hydrophobic	false
C7	CG1	ILE- 136	3.98	0	Hydrophobic	false
C8	CD1	ILE- 136	3.89	0	Hydrophobic	false
C9	CD1	ILE- 136	3.74	0	Hydrophobic	false