scPDB - 2woe entry

Protein Data Bank Entry:

PDB ID : 2woe

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2009-07-23

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	ADP-ribosyl-[dinitrogen reductase] glycohydrolase
ID:	DRAG_RHORU
AC:	P14300
Organism:	Rhodospirillum rubrum
Reign:	Bacteria
TaxID:	1085
EC Number:	3.2.2.24

Chains:

Chain Name:	Percentage of Residues within binding site
B	14 %
C	86 %

Ligand binding site composition:

B-Factor:	29.225
Number of residues:	46
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	1
Water Molecules:	4
Cofactors:
Metals:	MN

Cavity properties

Ligandability	Volume (Å3)
0.334	2234.250

% Hydrophobic	% Polar
34.59	65.41
According to VolSite

Ligand :

HET Code:	AR6
Formula:	C15H21N5O14P2
Molecular weight:	557.300 g/mol
DrugBank ID:	DB02059
Buried Surface Area:	69.84 %
Polar Surface area:	316.8 Å2

Number of
H-Bond Acceptors:	18
H-Bond Donors:	6
Rings:	4
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
-48.4947	10.2272	-2.91467

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
O2D	OD1	ASP- 60	2.95	156.25	H-Bond (Ligand Donor)	false
O2D	OD2	ASP- 60	3.27	126.6	H-Bond (Ligand Donor)	false
O1D	ND2	ASN- 97	2.78	131.7	H-Bond (Protein Donor)	false
O2A	N	THR- 101	3.07	129.67	H-Bond (Protein Donor)	false
O1B	N	CYS- 102	2.84	162.09	H-Bond (Protein Donor)	false
N6	O	GLU- 121	2.9	150.39	H-Bond (Ligand Donor)	false
N7	N	ALA- 124	3.36	136.52	H-Bond (Protein Donor)	false
O2B	N	GLY- 127	3.09	135.87	H-Bond (Protein Donor)	false
C2D	SD	MET- 130	3.89	0	Hydrophobic	false
O2B	NE2	HIS- 158	2.8	161.8	H-Bond (Protein Donor)	false
C4D	CB	ALA- 211	4.07	0	Hydrophobic	false
C5'	CB	ALA- 211	3.55	0	Hydrophobic	false
C1'	CB	TYR- 212	4.18	0	Hydrophobic	false
DuAr	DuAr	TYR- 212	3.87	0	Aromatic Face/Face	false
O3D	OD2	ASP- 243	2.6	159.65	H-Bond (Ligand Donor)	false
O2'	OD2	ASP- 273	2.83	129.63	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 273	3.36	171.95	H-Bond (Ligand Donor)	false
C2'	CD	LYS- 275	4.19	0	Hydrophobic	false
O2D	MN	MN- 400	2.35	0	Metal Acceptor	false
O3D	MN	MN- 400	2.36	0	Metal Acceptor	false
O2A	O	HOH- 2102	3.41	131.34	H-Bond (Protein Donor)	false
N6	O	HOH- 2114	3.34	129.6	H-Bond (Ligand Donor)	false