scPDB - 4kuk entry

Protein Data Bank Entry:

PDB ID : 4kuk

Resolution :1.500 Å

Experimental Method : X-ray

Deposition Date : 2013-05-22

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Putative blue-light photoreceptor
ID:	A8LP63_DINSH
AC:	A8LP63
Organism:	Dinoroseobacter shibae
Reign:	Bacteria
TaxID:	398580
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	14.481
Number of residues:	36
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.424	293.625

% Hydrophobic	% Polar
55.17	44.83
According to VolSite

Ligand :

HET Code:	RBF
Formula:	C17H20N4O6
Molecular weight:	376.364 g/mol
DrugBank ID:	DB00140
Buried Surface Area:	77.77 %
Polar Surface area:	155.04 Å2

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

Mass center Coordinates

X	Y	Z
10.4068	-2.85578	-4.73893

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
C6	CG2	VAL- 38	3.52	0	Hydrophobic	false
C7M	CB	SER- 40	4.13	0	Hydrophobic	false
C8M	CB	SER- 40	3.92	0	Hydrophobic	false
O2'	OD1	ASN- 71	2.69	167.54	H-Bond (Ligand Donor)	false
C9A	CB	CYS- 72	3.93	0	Hydrophobic	false
C2'	CB	ARG- 73	4.2	0	Hydrophobic	false
O5'	NH2	ARG- 73	3.03	157.72	H-Bond (Protein Donor)	false
N1	NE2	GLN- 76	3.44	142.98	H-Bond (Protein Donor)	false
O2	NE2	GLN- 76	3.1	155.39	H-Bond (Protein Donor)	false
O4'	NE2	GLN- 76	2.87	171.97	H-Bond (Protein Donor)	false
C5'	CG1	VAL- 85	4.05	0	Hydrophobic	false
C1'	CG2	ILE- 88	3.63	0	Hydrophobic	false
C4'	CG2	ILE- 88	4.03	0	Hydrophobic	false
C5'	CB	ARG- 89	3.78	0	Hydrophobic	false
C8M	CD2	LEU- 92	3.77	0	Hydrophobic	false
C9	CD1	LEU- 92	4.43	0	Hydrophobic	false
O2	ND2	ASN- 104	2.96	150.63	H-Bond (Protein Donor)	false
N3	OD1	ASN- 104	2.78	174.55	H-Bond (Ligand Donor)	false
O4	ND2	ASN- 114	3.13	127.12	H-Bond (Protein Donor)	false
C6	CD1	LEU- 116	4.43	0	Hydrophobic	false
C9A	CD2	LEU- 116	4.43	0	Hydrophobic	false
C9	CD1	ILE- 118	3.74	0	Hydrophobic	false
C7M	CB	PHE- 131	3.8	0	Hydrophobic	false
C8M	CB	PHE- 131	3.68	0	Hydrophobic	false
O4	NE2	GLN- 135	3.07	145.24	H-Bond (Protein Donor)	false
N5	NE2	GLN- 135	3.41	140.7	H-Bond (Protein Donor)	false
O2'	O	HOH- 313	3.01	141.26	H-Bond (Protein Donor)	false