scPDB - 2nom entry

Protein Data Bank Entry:

PDB ID : 2nom

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 2006-10-25

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Poly(A) polymerase, putative
ID:	Q381M1_TRYB2
AC:	Q381M1
Organism:	Trypanosoma brucei brucei
Reign:	Eukaryota
TaxID:	185431
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	22.542
Number of residues:	43
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	2
Water Molecules:	3
Cofactors:
Metals:	MG MG

Cavity properties

Ligandability	Volume (Å3)
0.817	1339.875

% Hydrophobic	% Polar
36.52	63.48
According to VolSite

Ligand :

HET Code:	DUT
Formula:	C9H11N2O14P3
Molecular weight:	464.110 g/mol
DrugBank ID:	DB02333
Buried Surface Area:	66.73 %
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
-19.3182	0.149607	-5.43204

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
C1'	CE2	PHE- 52	3.77	0	Hydrophobic	false
C4'	CD2	PHE- 52	3.85	0	Hydrophobic	false
O1B	N	SER- 54	3.17	155.37	H-Bond (Protein Donor)	false
O2G	OG	SER- 65	2.74	164.81	H-Bond (Protein Donor)	false
O2	ND2	ASN- 147	3.38	129.27	H-Bond (Protein Donor)	false
C2'	CB	ASN- 147	3.71	0	Hydrophobic	false
O3'	OG	SER- 148	3.17	159.15	H-Bond (Ligand Donor)	false
O2G	NZ	LYS- 169	2.86	176.52	H-Bond (Protein Donor)	false
O2G	NZ	LYS- 169	2.86	0	Ionic (Protein Cationic)	false
O1G	NZ	LYS- 173	3.2	134.93	H-Bond (Protein Donor)	false
O2G	NZ	LYS- 173	2.88	130.28	H-Bond (Protein Donor)	false
O1G	NZ	LYS- 173	3.2	0	Ionic (Protein Cationic)	false
O2G	NZ	LYS- 173	2.88	0	Ionic (Protein Cationic)	false
O1G	OG	SER- 188	2.59	142.25	H-Bond (Protein Donor)	false
O2A	N	TYR- 189	3.05	149.59	H-Bond (Protein Donor)	false
C3'	CD1	TYR- 189	3.4	0	Hydrophobic	false
O1B	MG	MG- 401	2.31	0	Metal Acceptor	false
O3G	MG	MG- 401	2.21	0	Metal Acceptor	false
O2	O	HOH- 525	2.65	148.46	H-Bond (Protein Donor)	false