scPDB - 3s87 entry

Protein Data Bank Entry:

PDB ID : 3s87

Resolution :2.250 Å

Experimental Method : X-ray

Deposition Date : 2011-05-27

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 large chain 1
ID:	RIR1_YEAST
AC:	P21524
Organism:	Saccharomyces cerevisiae
Reign:	Eukaryota
TaxID:	559292
EC Number:	1.17.4.1

Chains:

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

Ligand binding site composition:

B-Factor:	36.025
Number of residues:	22
Including
Standard Amino Acids:	21
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.331	351.000

% Hydrophobic	% Polar
53.85	46.15
According to VolSite

Ligand :

HET Code:	DGT
Formula:	C10H12N5O13P3
Molecular weight:	503.149 g/mol
DrugBank ID:	DB02181
Buried Surface Area:	42.58 %
Polar Surface area:	315.33 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	3
Rings:	3
Aromatic rings:	1
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
-10.7377	48.2822	23.6948

Binding mode :

What is Poseview ?

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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
O3'	OD2	ASP- 226	2.66	169.21	H-Bond (Ligand Donor)	false
O2A	N	ILE- 228	3.17	175.01	H-Bond (Protein Donor)	false
C2'	CD1	ILE- 228	3.83	0	Hydrophobic	false
C2'	CD1	ILE- 231	3.74	0	Hydrophobic	false
O1G	NH1	ARG- 256	3.46	120.69	H-Bond (Protein Donor)	false
O1G	NH2	ARG- 256	2.73	140.39	H-Bond (Protein Donor)	false
O3G	NH1	ARG- 256	2.7	171.28	H-Bond (Protein Donor)	false
O1G	CZ	ARG- 256	3.48	0	Ionic (Protein Cationic)	false
O3G	CZ	ARG- 256	3.62	0	Ionic (Protein Cationic)	false
C4'	CD	ARG- 256	3.69	0	Hydrophobic	false
C1'	CD1	ILE- 262	3.86	0	Hydrophobic	false
O3G	N	ALA- 263	2.73	170.67	H-Bond (Protein Donor)	false
O3B	N	GLY- 264	3.21	164.4	H-Bond (Protein Donor)	false
O1G	MG	MG- 2001	2.15	0	Metal Acceptor	false
O1B	MG	MG- 2001	2.08	0	Metal Acceptor	false
O1A	MG	MG- 2001	2.03	0	Metal Acceptor	false