scPDB - 3zc3 entry

Protein Data Bank Entry:

PDB ID : 3zc3

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2012-11-15

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
ID:	FENR_NOSSO
AC:	P21890
Organism:	Nostoc sp.
Reign:	Bacteria
TaxID:	1168
EC Number:	1.18.1.2

Chains:

Chain Name:	Percentage of Residues within binding site
A	80 %
B	20 %

Ligand binding site composition:

B-Factor:	30.289
Number of residues:	47
Including
Standard Amino Acids:	45
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:	FAD
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.349	2237.625

% Hydrophobic	% Polar
42.08	57.92
According to VolSite

Ligand :

HET Code:	NAP
Formula:	C21H25N7O17P3
Molecular weight:	740.381 g/mol
DrugBank ID:	DB03461
Buried Surface Area:	68.11 %
Polar Surface area:	405.54 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	5
Rings:	5
Aromatic rings:	3
Anionic atoms:	4
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
-34.4213	37.5085	-0.2825

Binding mode :

What is Poseview ?

2D View
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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
O1A	NH2	ARG- 100	3.26	133.36	H-Bond (Protein Donor)	false
O2N	NE	ARG- 100	2.71	156.4	H-Bond (Protein Donor)	false
O2N	NH2	ARG- 100	2.95	138.72	H-Bond (Protein Donor)	false
O2N	CZ	ARG- 100	3.27	0	Ionic (Protein Cationic)	false
C5D	CG	ARG- 100	3.85	0	Hydrophobic	false
C3D	CG	ARG- 100	4.31	0	Hydrophobic	false
O2A	NZ	LYS- 105	3.93	0	Ionic (Protein Cationic)	false
O2X	NZ	LYS- 105	3.12	0	Ionic (Protein Cationic)	false
C4D	CG	LYS- 105	4.45	0	Hydrophobic	false
O2X	NZ	LYS- 105	3.12	149.97	H-Bond (Protein Donor)	false
N7A	N	THR- 112	3.3	173.02	H-Bond (Protein Donor)	false
O7N	OG1	THR- 155	2.69	137.96	H-Bond (Protein Donor)	false
N7N	O	THR- 155	3.06	157.56	H-Bond (Ligand Donor)	false
C4B	CB	THR- 155	4.23	0	Hydrophobic	false
O1N	N	THR- 157	2.75	164.63	H-Bond (Protein Donor)	false
C3B	CB	PRO- 194	4.41	0	Hydrophobic	false
O3B	OG	SER- 223	2.74	161.47	H-Bond (Ligand Donor)	false
O3X	OG	SER- 223	2.55	161.36	H-Bond (Protein Donor)	false
C2B	CB	SER- 223	4.44	0	Hydrophobic	false
O2X	CZ	ARG- 224	3.78	0	Ionic (Protein Cationic)	false
O3X	CZ	ARG- 224	3.47	0	Ionic (Protein Cationic)	false
O2X	NH2	ARG- 224	2.87	140.62	H-Bond (Protein Donor)	false
O3X	NH2	ARG- 224	3.39	128.77	H-Bond (Protein Donor)	false
O3X	NE	ARG- 224	2.71	164.72	H-Bond (Protein Donor)	false
O1X	NH1	ARG- 233	3.1	137.85	H-Bond (Protein Donor)	false
O3X	CZ	ARG- 233	3.84	0	Ionic (Protein Cationic)	false
DuAr	DuAr	TYR- 235	3.57	0	Aromatic Face/Face	false
C1B	CE1	TYR- 235	3.66	0	Hydrophobic	false
N1A	NE2	GLN- 237	3.03	150.94	H-Bond (Protein Donor)	false
C1B	CD1	LEU- 263	4.34	0	Hydrophobic	false
C3N	CD2	LEU- 263	3.64	0	Hydrophobic	false
N7N	OH	TYR- 303	3.42	131.86	H-Bond (Ligand Donor)	false