scPDB - 1dnp entry

Protein Data Bank Entry:

PDB ID : 1dnp

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 1995-07-03

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_ECOLI
AC:	P00914
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	4.1.99.3

Chains:

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

Ligand binding site composition:

B-Factor:	12.808
Number of residues:	17
Including
Standard Amino Acids:	16
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.659	661.500

% Hydrophobic	% Polar
36.22	63.78
According to VolSite

Ligand :

HET Code:	MHF
Formula:	C20H21N7O6
Molecular weight:	455.424 g/mol
DrugBank ID:	-
Buried Surface Area:	34.62 %
Polar Surface area:	195.35 Å2

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

Mass center Coordinates

X	Y	Z
45.8358	37.8846	32.6098

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
C16	CG1	VAL- 107	4.3	0	Hydrophobic	false
O4	N	ASN- 108	2.73	152.12	H-Bond (Protein Donor)	false
NA2	OE2	GLU- 109	3.02	151.47	H-Bond (Ligand Donor)	false
N3	OE2	GLU- 109	3.32	135.98	H-Bond (Ligand Donor)	false
N3	OE1	GLU- 109	2.78	160.8	H-Bond (Ligand Donor)	false
C11	CB	CYS- 292	4.17	0	Hydrophobic	false
O1	NZ	LYS- 293	3.73	0	Ionic (Protein Cationic)	false
O2	NZ	LYS- 293	3.17	0	Ionic (Protein Cationic)	false
O2	NZ	LYS- 293	3.17	170.46	H-Bond (Protein Donor)	false
C17	CG	LYS- 293	3.71	0	Hydrophobic	false
C13	CB	LYS- 293	3.93	0	Hydrophobic	false
C16	CG	LYS- 293	3.74	0	Hydrophobic	false