scPDB - 3b9x entry

Protein Data Bank Entry:

PDB ID : 3b9x

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2007-11-07

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Pyrimidine-specific ribonucleoside hydrolase RihB
ID:	RIHB_ECOLI
AC:	P33022
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	3.2.2.8

Chains:

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

Ligand binding site composition:

B-Factor:	20.601
Number of residues:	28
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	CA

Cavity properties

Ligandability	Volume (Å3)
0.294	492.750

% Hydrophobic	% Polar
32.88	67.12
According to VolSite

Ligand :

HET Code:	NOS
Formula:	C10H12N4O5
Molecular weight:	268.226 g/mol
DrugBank ID:	DB04335
Buried Surface Area:	57.94 %
Polar Surface area:	133.75 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	2

Mass center Coordinates

X	Y	Z
4.84868	-15.8288	21.3697

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
O2'	OD1	ASP- 15	2.79	151.21	H-Bond (Ligand Donor)	false
O2'	ND2	ASN- 40	3.34	171.26	H-Bond (Protein Donor)	false
C3'	SD	MET- 150	3.35	0	Hydrophobic	false
O5'	ND2	ASN- 158	2.92	156.57	H-Bond (Protein Donor)	false
C5'	CG	GLU- 164	4.23	0	Hydrophobic	false
C4'	CD2	PHE- 165	4.49	0	Hydrophobic	false
O3'	ND2	ASN- 166	3.14	141.02	H-Bond (Protein Donor)	false
C5'	CD2	LEU- 189	4.47	0	Hydrophobic	false
O6	NE2	GLN- 227	2.73	132.78	H-Bond (Protein Donor)	false
N7	NE2	GLN- 227	3.28	132.69	H-Bond (Protein Donor)	false
N1	OH	TYR- 231	3.21	150.4	H-Bond (Protein Donor)	false
C3'	CB	HIS- 239	4.14	0	Hydrophobic	false
O3'	OD1	ASP- 240	2.54	170.07	H-Bond (Ligand Donor)	false
O3'	OD2	ASP- 240	2.99	121.95	H-Bond (Ligand Donor)	false
O2'	CA	CA- 400	2.43	0	Metal Acceptor	false
O3'	CA	CA- 400	2.74	0	Metal Acceptor	false