scPDB - 3tba entry

Protein Data Bank Entry:

PDB ID : 3tba

Resolution :2.800 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:	52.484
Number of residues:	31
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.690	546.750

% Hydrophobic	% Polar
40.74	59.26
According to VolSite

Ligand :

HET Code:	ADP
Formula:	C10H12N5O10P2
Molecular weight:	424.177 g/mol
DrugBank ID:	-
Buried Surface Area:	64.09 %
Polar Surface area:	260.7 Å2

Number of
H-Bond Acceptors:	14
H-Bond Donors:	3
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
22.4178	51.9997	17.2973

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
O2B	N	SER- 202	3.28	171.04	H-Bond (Protein Donor)	false
O3B	OG	SER- 202	2.7	174.48	H-Bond (Protein Donor)	false
C4'	CB	SER- 217	4.4	0	Hydrophobic	false
C1'	CB	SER- 217	4.31	0	Hydrophobic	false
O2'	O	SER- 217	2.66	145.83	H-Bond (Ligand Donor)	false
C3'	SG	CYS- 218	4.24	0	Hydrophobic	false
C2'	CB	LEU- 427	3.9	0	Hydrophobic	false
C3'	SG	CYS- 428	3.76	0	Hydrophobic	false
O3'	OE1	GLU- 430	2.84	176.57	H-Bond (Ligand Donor)	false
C4'	CD1	LEU- 445	4.34	0	Hydrophobic	false
C5'	CG	PRO- 607	4.38	0	Hydrophobic	false
O1B	N	SER- 610	3.45	145.28	H-Bond (Protein Donor)	false
O3B	OG	SER- 610	3.04	169.48	H-Bond (Protein Donor)	false
O1B	OG1	THR- 611	2.69	152.35	H-Bond (Protein Donor)	false
O1B	N	THR- 611	3.08	165.2	H-Bond (Protein Donor)	false