scPDB - 3mkn entry

Protein Data Bank Entry:

PDB ID : 3mkn

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2010-04-15

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:	C3T3U2_ECOLX
AC:	C3T3U2
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	562
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	34.639
Number of residues:	26
Including
Standard Amino Acids:	24
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	CA

Cavity properties

Ligandability	Volume (Å3)
0.713	452.250

% Hydrophobic	% Polar
50.00	50.00
According to VolSite

Ligand :

HET Code:	DNB
Formula:	C11H18N3O3
Molecular weight:	240.279 g/mol
DrugBank ID:	-
Buried Surface Area:	75.95 %
Polar Surface area:	129.34 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	6
Rings:	2
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	2

Mass center Coordinates

X	Y	Z
25.6769	3.29118	32.9139

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	2.69	152.26	H-Bond (Ligand Donor)	false
O2'	ND2	ASN- 40	3.15	178.09	H-Bond (Protein Donor)	false
C5	CB	ALA- 78	3.84	0	Hydrophobic	false
C4	CG1	ILE- 81	3.73	0	Hydrophobic	false
C3'	SD	MET- 150	3.75	0	Hydrophobic	false
C5'	SD	MET- 150	3.71	0	Hydrophobic	false
O5'	ND2	ASN- 158	2.88	163.6	H-Bond (Protein Donor)	false
N4'	OE2	GLU- 164	3.77	0	Ionic (Ligand Cationic)	false
C5'	CG	GLU- 164	4.48	0	Hydrophobic	false
O5'	OE2	GLU- 164	2.58	156.56	H-Bond (Ligand Donor)	false
C6	CB	PHE- 165	3.56	0	Hydrophobic	false
O3'	ND2	ASN- 166	3.24	151.74	H-Bond (Protein Donor)	false
N4'	OD1	ASN- 166	3.15	152.74	H-Bond (Ligand Donor)	false
C5'	CD2	LEU- 189	4.22	0	Hydrophobic	false
C3'	CB	HIS- 239	4.11	0	Hydrophobic	false
C5'	CB	HIS- 239	4.46	0	Hydrophobic	false
N4'	O	HOH- 314	3.02	132	H-Bond (Ligand Donor)	false
O2'	CA	CA- 501	2.59	0	Metal Acceptor	false
O3'	CA	CA- 501	2.7	0	Metal Acceptor	false