scPDB - 2j08 entry

Protein Data Bank Entry:

PDB ID : 2j08

Resolution :2.610 Å

Experimental Method : X-ray

Deposition Date : 2006-08-01

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Deoxyribodipyrimidine photo-lyase
ID:	PHR_THET8
AC:	P61497
Organism:	Thermus thermophilus
Reign:	Bacteria
TaxID:	300852
EC Number:	4.1.99.3

Chains:

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

Ligand binding site composition:

B-Factor:	19.675
Number of residues:	37
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.146	1184.625

% Hydrophobic	% Polar
40.46	59.54
According to VolSite

Ligand :

HET Code:	IRF
Formula:	C16H17IN4O6
Molecular weight:	488.234 g/mol
DrugBank ID:	-
Buried Surface Area:	56.48 %
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
44.8348	12.2062	31.7928

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
C3'	CB	ARG- 9	4.18	0	Hydrophobic	false
O4'	N	GLY- 10	3.09	135.98	H-Bond (Protein Donor)	false
N3	O	VAL- 34	2.74	162.78	H-Bond (Ligand Donor)	false
O4	N	ASP- 36	3.2	168.91	H-Bond (Protein Donor)	false
C6	CB	ASN- 39	4.05	0	Hydrophobic	false
C9A	CB	ASN- 39	4.08	0	Hydrophobic	false
C6	CD2	LEU- 40	4.2	0	Hydrophobic	false
C7M	CB	ARG- 46	3.83	0	Hydrophobic	false
C6	CB	PHE- 50	3.74	0	Hydrophobic	false
C5'	CB	SER- 96	3.82	0	Hydrophobic	false
O3'	NH1	ARG- 104	2.52	166.69	H-Bond (Protein Donor)	false
O5'	NH2	ARG- 104	3.33	148.83	H-Bond (Protein Donor)	false
I8	CD2	LEU- 218	4.05	0	Hydrophobic	false
C8	CD2	LEU- 218	3.59	0	Hydrophobic	false
O2	O	HOH- 2104	2.53	179.97	H-Bond (Protein Donor)	false
O5'	O	HOH- 2106	2.86	179.97	H-Bond (Protein Donor)	false