scPDB - 2cvy entry

Protein Data Bank Entry:

PDB ID : 2cvy

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 2005-06-14

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:	41.895
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)
0.186	313.875

% Hydrophobic	% Polar
54.84	45.16
According to VolSite

Ligand :

HET Code:	TTP
Formula:	C10H13N2O14P3
Molecular weight:	478.137 g/mol
DrugBank ID:	DB02452
Buried Surface Area:	49.57 %
Polar Surface area:	279.44 Å2

Number of
H-Bond Acceptors:	14
H-Bond Donors:	2
Rings:	2
Aromatic rings:	0
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
-10.001	47.6882	22.4731

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
O1A	N	ILE- 228	3.1	159.67	H-Bond (Protein Donor)	false
C2'	CD1	ILE- 228	4.08	0	Hydrophobic	false
C5M	CG1	ILE- 228	3.8	0	Hydrophobic	false
C2'	CD1	ILE- 231	3.65	0	Hydrophobic	false
O2G	NH1	ARG- 256	2.93	155.74	H-Bond (Protein Donor)	false
O3G	NH2	ARG- 256	3.39	156.97	H-Bond (Protein Donor)	false
O2G	CZ	ARG- 256	3.96	0	Ionic (Protein Cationic)	false
O3G	CZ	ARG- 256	3.97	0	Ionic (Protein Cationic)	false
C4'	CD	ARG- 256	3.67	0	Hydrophobic	false
C1'	CD1	ILE- 262	4.24	0	Hydrophobic	false
O1G	N	ALA- 263	3.43	128.92	H-Bond (Protein Donor)	false
O2G	N	ALA- 263	2.58	160.87	H-Bond (Protein Donor)	false
C1'	CB	SER- 269	4.31	0	Hydrophobic	false
O2	N	ASN- 270	3.41	168.66	H-Bond (Protein Donor)	false
O2A	MG	MG- 2001	2.33	0	Metal Acceptor	false
O3B	MG	MG- 2001	2.5	0	Metal Acceptor	false