scPDB - 5cns entry

Protein Data Bank Entry:

PDB ID : 5cns

Resolution :2.980 Å

Experimental Method : X-ray

Deposition Date : 2015-07-18

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Ribonucleoside-diphosphate reductase 1 subunit alpha
ID:	RIR1_ECOLI
AC:	P00452
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	1.17.4.1

Chains:

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

Ligand binding site composition:

B-Factor:	55.571
Number of residues:	28
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.047	445.500

% Hydrophobic	% Polar
45.45	54.55
According to VolSite

Ligand :

HET Code:	DAT
Formula:	C10H12N5O9P2
Molecular weight:	408.178 g/mol
DrugBank ID:	-
Buried Surface Area:	73.68 %
Polar Surface area:	240.48 Å2

Number of
H-Bond Acceptors:	13
H-Bond Donors:	2
Rings:	3
Aromatic rings:	2
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
-15.9274	-64.9577	-3.78308

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
O1B	NZ	LYS- 9	2.93	156.99	H-Bond (Protein Donor)	false
N7	NZ	LYS- 9	3.4	138.05	H-Bond (Protein Donor)	false
O1B	NZ	LYS- 9	2.93	0	Ionic (Protein Cationic)	false
O2B	NZ	LYS- 9	3.53	0	Ionic (Protein Cationic)	false
O2B	N	ARG- 10	3.34	147.61	H-Bond (Protein Donor)	false
O2A	NE	ARG- 10	2.7	161.16	H-Bond (Protein Donor)	false
O2A	NH2	ARG- 10	3.09	134.5	H-Bond (Protein Donor)	false
O2A	CZ	ARG- 10	3.32	0	Ionic (Protein Cationic)	false
N6	OE2	GLU- 15	3.26	163.54	H-Bond (Ligand Donor)	false
N6	O	ARG- 16	2.88	150.34	H-Bond (Ligand Donor)	false
N1	N	ASN- 18	2.95	163.46	H-Bond (Protein Donor)	false
C2'	CB	LYS- 21	4.38	0	Hydrophobic	false
C1'	CG1	ILE- 22	4.4	0	Hydrophobic	false
C3'	CG1	VAL- 25	3.89	0	Hydrophobic	false
O4'	OG1	THR- 55	2.66	124.56	H-Bond (Protein Donor)	false
C1'	CG2	ILE- 58	4.21	0	Hydrophobic	false
O3'	ND1	HIS- 59	2.81	171.31	H-Bond (Ligand Donor)	false
C4'	CB	HIS- 59	3.72	0	Hydrophobic	false
C5'	CE2	PHE- 87	4.42	0	Hydrophobic	false
O1A	NZ	LYS- 91	2.79	0	Ionic (Protein Cationic)	false
O2A	NZ	LYS- 91	2.95	0	Ionic (Protein Cationic)	false
O2A	NZ	LYS- 91	2.95	145.83	H-Bond (Protein Donor)	false
O1B	MG	MG- 803	2.1	0	Metal Acceptor	false
O1A	MG	MG- 803	2.09	0	Metal Acceptor	false