scPDB - 1fnd entry

Protein Data Bank Entry:

PDB ID : 1fnd

Resolution :1.700 Å

Experimental Method : X-ray

Deposition Date : 1995-01-05

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Ferredoxin--NADP reductase, chloroplastic
ID:	FENR_SPIOL
AC:	P00455
Organism:	Spinacia oleracea
Reign:	Eukaryota
TaxID:	3562
EC Number:	1.18.1.2

Chains:

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

Ligand binding site composition:

B-Factor:	27.140
Number of residues:	29
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.937	418.500

% Hydrophobic	% Polar
63.71	36.29
According to VolSite

Ligand :

HET Code:	A2P
Formula:	C10H11N5O10P2
Molecular weight:	423.169 g/mol
DrugBank ID:	DB02098
Buried Surface Area:	54.78 %
Polar Surface area:	263.53 Å2

Number of
H-Bond Acceptors:	14
H-Bond Donors:	2
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
11.2477	-1.81915	12.9488

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
O4P	NZ	LYS- 116	3.63	0	Ionic (Protein Cationic)	false
O6P	NZ	LYS- 116	3.55	0	Ionic (Protein Cationic)	false
C4'	CB	THR- 170	4.3	0	Hydrophobic	false
C3'	CB	PRO- 205	4.21	0	Hydrophobic	false
O3P	OG	SER- 234	2.73	162.91	H-Bond (Protein Donor)	false
O3'	OG	SER- 234	2.95	151.1	H-Bond (Ligand Donor)	false
O2P	CZ	ARG- 235	3.53	0	Ionic (Protein Cationic)	false
O3P	CZ	ARG- 235	3.58	0	Ionic (Protein Cationic)	false
O2P	NH2	ARG- 235	2.58	149.65	H-Bond (Protein Donor)	false
O3P	NH2	ARG- 235	3.46	131.45	H-Bond (Protein Donor)	false
O3P	NE	ARG- 235	2.78	177.72	H-Bond (Protein Donor)	false
O1P	NZ	LYS- 244	3.06	123.14	H-Bond (Protein Donor)	false
O3P	NZ	LYS- 244	2.97	157.62	H-Bond (Protein Donor)	false
O1P	NZ	LYS- 244	3.06	0	Ionic (Protein Cationic)	false
O3P	NZ	LYS- 244	2.97	0	Ionic (Protein Cationic)	false
O1P	OH	TYR- 246	2.68	149.81	H-Bond (Protein Donor)	false
C1'	CE1	TYR- 246	4.05	0	Hydrophobic	false
C5'	CD1	LEU- 274	4.04	0	Hydrophobic	false