scPDB - 2dvo entry

Protein Data Bank Entry:

PDB ID : 2dvo

Resolution :2.210 Å

Experimental Method : X-ray

Deposition Date : 2006-07-31

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	dITP/XTP pyrophosphatase
ID:	NTPA_PYRHO
AC:	O59580
Organism:	Pyrococcus horikoshii
Reign:	Archaea
TaxID:	70601
EC Number:	3.6.1.19

Chains:

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

Ligand binding site composition:

B-Factor:	21.685
Number of residues:	44
Including
Standard Amino Acids:	40
Non Standard Amino Acids:	1
Water Molecules:	3
Cofactors:
Metals:	NA

Cavity properties

Ligandability	Volume (Å3)
0.114	513.000

% Hydrophobic	% Polar
39.47	60.53
According to VolSite

Ligand :

HET Code:	ITT
Formula:	C10H11N4O14P3
Molecular weight:	504.134 g/mol
DrugBank ID:	-
Buried Surface Area:	71.63 %
Polar Surface area:	314.09 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
50.7433	64.9841	35.9985

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
O1G	OG1	THR- 7	2.66	157.96	H-Bond (Protein Donor)	false
O3G	N	SER- 8	2.79	161.41	H-Bond (Protein Donor)	false
O3G	OG	SER- 8	3.27	163.2	H-Bond (Protein Donor)	false
O1B	ND2	ASN- 9	2.73	162.19	H-Bond (Protein Donor)	false
O1G	NZ	LYS- 12	2.81	169.68	H-Bond (Protein Donor)	false
O2A	NZ	LYS- 12	2.62	169.4	H-Bond (Protein Donor)	false
O1G	NZ	LYS- 12	2.81	0	Ionic (Protein Cationic)	false
O2A	NZ	LYS- 12	2.62	0	Ionic (Protein Cationic)	false
O2G	OE2	GLU- 36	2.71	162.24	H-Bond (Protein Donor)	false
O2A	N	SER- 66	3.4	148.62	H-Bond (Protein Donor)	false
C1'	CB	SER- 81	4.16	0	Hydrophobic	false
C4'	CB	SER- 81	3.54	0	Hydrophobic	false
C4'	CB	SER- 82	4.01	0	Hydrophobic	false
C2'	CE1	PHE- 140	4.01	0	Hydrophobic	false
C1'	CD2	TYR- 142	4.22	0	Hydrophobic	false
N3	N	TYR- 142	3.29	151.18	H-Bond (Protein Donor)	false
O6	NZ	LYS- 163	2.68	147.18	H-Bond (Protein Donor)	false
N7	NE2	HIS- 168	3.18	162.03	H-Bond (Protein Donor)	false
N7	NH2	ARG- 169	2.76	168.92	H-Bond (Protein Donor)	false
O6	NH1	ARG- 169	3.09	150.44	H-Bond (Protein Donor)	false
O1A	O	HOH- 307	3.26	179.97	H-Bond (Protein Donor)	false
O1G	O	HOH- 325	2.88	165.8	H-Bond (Protein Donor)	false