scPDB - 3jyn entry

Protein Data Bank Entry:

PDB ID : 3jyn

Resolution :2.010 Å

Experimental Method : X-ray

Deposition Date : 2009-09-22

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Quinone oxidoreductase
ID:	Q88B47_PSESM
AC:	Q88B47
Organism:	Pseudomonas syringae pv. tomato
Reign:	Bacteria
TaxID:	223283
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	23.002
Number of residues:	51
Including
Standard Amino Acids:	49
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.454	1144.125

% Hydrophobic	% Polar
51.62	48.38
According to VolSite

Ligand :

HET Code:	NDP
Formula:	C21H26N7O17P3
Molecular weight:	741.389 g/mol
DrugBank ID:	DB02338
Buried Surface Area:	69.46 %
Polar Surface area:	404.9 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	5
Rings:	5
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
24.8098	-3.99981	15.6767

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
C5B	CE2	PHE- 42	3.48	0	Hydrophobic	false
C2D	CB	PHE- 42	3.65	0	Hydrophobic	false
O2N	N	PHE- 42	3.23	162.63	H-Bond (Protein Donor)	false
C5N	CD2	LEU- 123	3.33	0	Hydrophobic	false
C4N	CG2	THR- 127	3.77	0	Hydrophobic	false
O7N	OH	TYR- 130	2.77	168.47	H-Bond (Protein Donor)	false
C4B	CB	ALA- 148	4.2	0	Hydrophobic	false
C1B	CB	ALA- 148	3.79	0	Hydrophobic	false
O1A	N	GLY- 152	2.84	156.61	H-Bond (Protein Donor)	false
O2A	N	GLY- 152	3.33	133.15	H-Bond (Protein Donor)	false
O1N	N	VAL- 153	2.68	136	H-Bond (Protein Donor)	false
C5D	CG2	VAL- 153	3.82	0	Hydrophobic	false
O1X	N	SER- 173	3.27	135.73	H-Bond (Protein Donor)	false
O3X	OG	SER- 173	2.75	168.98	H-Bond (Protein Donor)	false
O1X	NZ	LYS- 177	3.62	0	Ionic (Protein Cationic)	false
O3X	NZ	LYS- 177	2.73	0	Ionic (Protein Cationic)	false
O3X	NZ	LYS- 177	2.73	158.77	H-Bond (Protein Donor)	false
O2X	OH	TYR- 192	2.51	165.05	H-Bond (Protein Donor)	false
O3D	O	GLY- 216	2.61	145.4	H-Bond (Ligand Donor)	false
C4D	CE2	PHE- 238	3.98	0	Hydrophobic	false
N7N	O	PHE- 238	3.07	164.67	H-Bond (Ligand Donor)	false
O3D	N	ASN- 240	3.22	128.49	H-Bond (Protein Donor)	false
C5B	CB	ALA- 241	4.39	0	Hydrophobic	false
C1B	CB	ALA- 241	4.38	0	Hydrophobic	false
O3D	N	ALA- 241	3.43	122.47	H-Bond (Protein Donor)	false
N7N	O	PRO- 264	3.03	154.62	H-Bond (Ligand Donor)	false
O7N	N	LEU- 266	2.6	127.59	H-Bond (Protein Donor)	false
C3B	CB	ARG- 315	4.06	0	Hydrophobic	false
C2B	CG	ARG- 315	4.02	0	Hydrophobic	false
O2X	CZ	ARG- 315	3.57	0	Ionic (Protein Cationic)	false
O3X	CZ	ARG- 315	3.67	0	Ionic (Protein Cationic)	false
O2X	NH2	ARG- 315	2.67	154.21	H-Bond (Protein Donor)	false
O3X	NE	ARG- 315	3.21	140.69	H-Bond (Protein Donor)	false
O3X	NH2	ARG- 315	3.31	135.45	H-Bond (Protein Donor)	false
O2A	O	HOH- 331	2.72	151.11	H-Bond (Protein Donor)	false
O3B	O	HOH- 374	2.84	179.97	H-Bond (Protein Donor)	false