scPDB - 2nnl entry

Protein Data Bank Entry:

PDB ID : 2nnl

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2006-10-24

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Dihydroflavonol 4-reductase
ID:	DFRA_VITVI
AC:	P51110
Organism:	Vitis vinifera
Reign:	Eukaryota
TaxID:	29760
EC Number:	1.1.1.219

Chains:

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

Ligand binding site composition:

B-Factor:	29.922
Number of residues:	36
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:	NAP
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.202	654.750

% Hydrophobic	% Polar
56.70	43.30
According to VolSite

Ligand :

HET Code:	ERD
Formula:	C15H11O6
Molecular weight:	287.244 g/mol
DrugBank ID:	-
Buried Surface Area:	77.62 %
Polar Surface area:	110.05 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	1

Mass center Coordinates

X	Y	Z
76.276	67.7352	40.2308

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
C1	CE	MET- 88	4.09	0	Hydrophobic	false
O13	OG	SER- 128	3.09	166.96	H-Bond (Protein Donor)	false
C17	CB	ALA- 129	3.84	0	Hydrophobic	false
O24	ND2	ASN- 133	2.95	131.33	H-Bond (Protein Donor)	false
O13	OH	TYR- 163	2.81	167.01	H-Bond (Protein Donor)	false
C11	CE1	PHE- 164	4.04	0	Hydrophobic	false
C16	CB	THR- 191	4.35	0	Hydrophobic	false
C15	CB	LEU- 192	4.25	0	Hydrophobic	false
C4	CD1	LEU- 192	3.52	0	Hydrophobic	false
C1	CB	SER- 205	4.17	0	Hydrophobic	false
C5	CB	THR- 208	4.07	0	Hydrophobic	false
C4	CG2	ILE- 222	4.29	0	Hydrophobic	false
C5	CD1	ILE- 222	3.86	0	Hydrophobic	false
C14	CG2	ILE- 222	3.87	0	Hydrophobic	false
C10	C4N	NAP- 1330	3.56	0	Hydrophobic	false