scPDB - 2oby entry

Protein Data Bank Entry:

PDB ID : 2oby

Resolution :3.000 Å

Experimental Method : X-ray

Deposition Date : 2006-12-20

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Quinone oxidoreductase PIG3
ID:	QORX_HUMAN
AC:	Q53FA7
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	1

Chains:

Chain Name:	Percentage of Residues within binding site
A	2 %
B	98 %

Ligand binding site composition:

B-Factor:	48.597
Number of residues:	55
Including
Standard Amino Acids:	55
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.215	864.000

% Hydrophobic	% Polar
51.17	48.83
According to VolSite

Ligand :

HET Code:	NAP
Formula:	C21H25N7O17P3
Molecular weight:	740.381 g/mol
DrugBank ID:	DB03461
Buried Surface Area:	65.72 %
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
-7.44229	34.5362	-12.5421

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
O1A	NH1	ARG- 41	3.32	159.18	H-Bond (Protein Donor)	false
O1N	N	ARG- 41	2.98	155.17	H-Bond (Protein Donor)	false
C5B	CD	ARG- 41	4.46	0	Hydrophobic	false
C3D	CB	ARG- 41	4.02	0	Hydrophobic	false
C5N	CG	GLU- 123	3.96	0	Hydrophobic	false
C4N	CG2	THR- 127	3.98	0	Hydrophobic	false
C4B	CB	ALA- 148	4.09	0	Hydrophobic	false
C1B	CB	ALA- 148	4.04	0	Hydrophobic	false
C5D	CB	SER- 151	4.47	0	Hydrophobic	false
C5B	CB	SER- 151	3.85	0	Hydrophobic	false
O2A	N	GLY- 152	3.24	154.43	H-Bond (Protein Donor)	false
O2N	N	GLY- 152	2.72	120.19	H-Bond (Protein Donor)	false
O2N	N	VAL- 153	3.41	149.89	H-Bond (Protein Donor)	false
C5N	CG2	VAL- 153	4.25	0	Hydrophobic	false
O2X	N	GLY- 173	3.43	128.42	H-Bond (Protein Donor)	false
O3X	N	GLY- 173	3.03	130.98	H-Bond (Protein Donor)	false
O3B	NZ	LYS- 177	3.3	132.71	H-Bond (Protein Donor)	false
O2B	NZ	LYS- 177	3.26	121.77	H-Bond (Protein Donor)	false
O2X	NZ	LYS- 177	3.4	172.72	H-Bond (Protein Donor)	false
O2X	NZ	LYS- 177	3.4	0	Ionic (Protein Cationic)	false
O1X	OH	TYR- 192	2.63	166.09	H-Bond (Protein Donor)	false
C4D	CB	CYS- 216	4.03	0	Hydrophobic	false
C4D	CE2	TYR- 238	4.35	0	Hydrophobic	false
C5B	SD	MET- 241	4.17	0	Hydrophobic	false
C3D	SD	MET- 241	3.85	0	Hydrophobic	false
N7N	O	SER- 264	3.27	138.01	H-Bond (Ligand Donor)	false
C2B	CB	ASN- 320	3.75	0	Hydrophobic	false
O2A	ND2	ASN- 322	3.03	143.29	H-Bond (Protein Donor)	false