scPDB - 3tb9 entry

Protein Data Bank Entry:

PDB ID : 3tb9

Resolution :2.530 Å

Experimental Method : X-ray

Deposition Date : 2011-08-05

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:	35.124
Number of residues:	30
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.486	340.875

% Hydrophobic	% Polar
41.58	58.42
According to VolSite

Ligand :

HET Code:	CDP
Formula:	C9H12N3O11P2
Molecular weight:	400.153 g/mol
DrugBank ID:	DB04555
Buried Surface Area:	63.13 %
Polar Surface area:	249.77 Å2

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

Mass center Coordinates

X	Y	Z
23.2279	51.4677	16.3607

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
O3B	OG	SER- 202	2.66	173.06	H-Bond (Protein Donor)	false
O2B	N	SER- 202	2.9	166.24	H-Bond (Protein Donor)	false
C4'	CB	SER- 217	3.72	0	Hydrophobic	false
C1'	CB	SER- 217	4.27	0	Hydrophobic	false
O2'	O	SER- 217	2.82	157.6	H-Bond (Ligand Donor)	false
C3'	SG	CYS- 218	3.92	0	Hydrophobic	false
C2'	CD2	LEU- 427	4.08	0	Hydrophobic	false
C3'	SG	CYS- 428	3.31	0	Hydrophobic	false
O3'	OE1	GLU- 430	2.63	147.41	H-Bond (Ligand Donor)	false
C5'	CD2	LEU- 445	3.38	0	Hydrophobic	false
C5'	CB	MET- 606	4.15	0	Hydrophobic	false
O1A	N	THR- 608	2.73	138.68	H-Bond (Protein Donor)	false
O2A	N	ALA- 609	2.98	155.88	H-Bond (Protein Donor)	false
O1B	N	SER- 610	3.23	137.95	H-Bond (Protein Donor)	false
O1B	N	THR- 611	3.15	170.45	H-Bond (Protein Donor)	false
O1B	OG1	THR- 611	2.85	165.96	H-Bond (Protein Donor)	false
O2'	O	HOH- 989	2.59	179.97	H-Bond (Protein Donor)	false