scPDB - 1qnf entry

Protein Data Bank Entry:

PDB ID : 1qnf

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 1997-07-04

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_SYNP6
AC:	P05327
Organism:	Synechococcus sp.
Reign:	Bacteria
TaxID:	269084
EC Number:	4.1.99.3

Chains:

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

Ligand binding site composition:

B-Factor:	14.597
Number of residues:	34
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.231	779.625

% Hydrophobic	% Polar
56.28	43.72
According to VolSite

Ligand :

HET Code:	HDF
Formula:	C16H17N3O7
Molecular weight:	363.322 g/mol
DrugBank ID:	-
Buried Surface Area:	74.52 %
Polar Surface area:	162.91 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	6
Rings:	3
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
43.9242	8.49254	65.0593

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- 10	4.04	0	Hydrophobic	false
C2'	CB	ARG- 11	4.06	0	Hydrophobic	false
N3	O	CYS- 36	2.81	163.36	H-Bond (Ligand Donor)	false
O4	N	ASP- 38	3.08	172	H-Bond (Protein Donor)	false
C3'	CD1	ILE- 41	4.46	0	Hydrophobic	false
C5A	CG2	ILE- 41	3.56	0	Hydrophobic	false
C6	CD2	LEU- 42	4.3	0	Hydrophobic	false
C8	CE	MET- 47	4.42	0	Hydrophobic	false
C7	SD	MET- 47	3.59	0	Hydrophobic	false
O8	NE	ARG- 51	2.97	157.55	H-Bond (Protein Donor)	false
C6	CD2	LEU- 55	3.6	0	Hydrophobic	false
O5'	OE1	GLU- 103	2.89	137.8	H-Bond (Ligand Donor)	false
C5'	CD2	TYR- 105	4.42	0	Hydrophobic	false
O3'	NH1	ARG- 109	2.97	158.94	H-Bond (Protein Donor)	false
O4'	NH2	ARG- 109	3.23	146.04	H-Bond (Protein Donor)	false
O8	NZ	LYS- 248	2.88	166.54	H-Bond (Protein Donor)	false
C1'	CE1	PHE- 249	4.23	0	Hydrophobic	false
O2	O	HOH- 636	2.75	172.04	H-Bond (Protein Donor)	false
O2	O	HOH- 647	3.05	134.51	H-Bond (Protein Donor)	false