scPDB - 2yvp entry

Protein Data Bank Entry:

PDB ID : 2yvp

Resolution :1.660 Å

Experimental Method : X-ray

Deposition Date : 2007-04-13

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	MutT/nudix family protein
ID:	Q5SJY9_THET8
AC:	Q5SJY9
Organism:	Thermus thermophilus
Reign:	Bacteria
TaxID:	300852
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	13.799
Number of residues:	38
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	3
Water Molecules:	3
Cofactors:
Metals:	MG MG MG

Cavity properties

Ligandability	Volume (Å3)
0.012	499.500

% Hydrophobic	% Polar
47.97	52.03
According to VolSite

Ligand :

HET Code:	RBY
Formula:	C16H23N5O13P2
Molecular weight:	555.327 g/mol
DrugBank ID:	-
Buried Surface Area:	44.63 %
Polar Surface area:	307.57 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	6
Rings:	4
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
14.297	33.7654	63.7106

Binding mode :

What is Poseview ?

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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
CR5	CB	ALA- 43	4.07	0	Hydrophobic	false
CR5	CZ	PHE- 45	4.25	0	Hydrophobic	false
O1B	CZ	ARG- 62	3.9	0	Ionic (Protein Cationic)	false
O2B	CZ	ARG- 62	3.84	0	Ionic (Protein Cationic)	false
O1B	NH1	ARG- 62	2.97	172.47	H-Bond (Protein Donor)	false
O2B	NH2	ARG- 62	2.98	166.61	H-Bond (Protein Donor)	false
O2A	N	LYS- 76	2.72	169.14	H-Bond (Protein Donor)	false
CR5	CZ	PHE- 119	4.5	0	Hydrophobic	false
CR2	CE1	PHE- 119	4.28	0	Hydrophobic	false
CR1	CZ	PHE- 119	3.73	0	Hydrophobic	false
C5'	CG	GLU- 136	3.97	0	Hydrophobic	false
C4'	CB	GLU- 136	4.45	0	Hydrophobic	false
C3'	CG	GLU- 139	3.49	0	Hydrophobic	false
C5'	CG	GLU- 139	3.79	0	Hydrophobic	false
O1A	MG	MG- 183	2.1	0	Metal Acceptor	false
O2B	MG	MG- 184	2.2	0	Metal Acceptor	false
O1A	MG	MG- 184	2.25	0	Metal Acceptor	false
O2A	MG	MG- 185	2.54	0	Metal Acceptor	false