scPDB - 3er9 entry

Protein Data Bank Entry:

PDB ID : 3er9

Resolution :2.060 Å

Experimental Method : X-ray

Deposition Date : 2008-10-01

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 catalytic subunit
ID:	PAP1_VACCW
AC:	P23371
Organism:	Vaccinia virus )
Reign:	Viruses
TaxID:	10254
EC Number:	2.7.7.19

Chains:

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

Ligand binding site composition:

B-Factor:	33.869
Number of residues:	36
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	2
Water Molecules:	2
Cofactors:
Metals:	CA CA

Cavity properties

Ligandability	Volume (Å3)
0.328	870.750

% Hydrophobic	% Polar
40.70	59.30
According to VolSite

Ligand :

HET Code:	3AT
Formula:	C10H12N5O12P3
Molecular weight:	487.150 g/mol
DrugBank ID:	DB01860
Buried Surface Area:	55.75 %
Polar Surface area:	299.64 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	2
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
18.6056	13.6884	18.7356

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
O2G	OG	SER- 188	2.52	171.93	H-Bond (Protein Donor)	false
O1B	N	SER- 188	3.26	173.81	H-Bond (Protein Donor)	false
O2G	N	GLY- 201	3.2	165.24	H-Bond (Protein Donor)	false
C2'	CB	ASN- 284	3.8	0	Hydrophobic	false
C5'	SD	MET- 288	4.43	0	Hydrophobic	false
C3'	SD	MET- 288	3.59	0	Hydrophobic	false
O2A	CZ	ARG- 294	3.75	0	Ionic (Protein Cationic)	false
O2A	NH1	ARG- 294	2.86	174.57	H-Bond (Protein Donor)	false
O1G	NZ	LYS- 304	3.05	153.51	H-Bond (Protein Donor)	false
O3B	NZ	LYS- 304	3.14	123.77	H-Bond (Protein Donor)	false
O1G	NZ	LYS- 304	3.05	0	Ionic (Protein Cationic)	false
O2G	NH2	ARG- 308	2.78	159.61	H-Bond (Protein Donor)	false
O2B	NE	ARG- 308	2.8	152.98	H-Bond (Protein Donor)	false
O2G	CZ	ARG- 308	3.81	0	Ionic (Protein Cationic)	false
O2B	CZ	ARG- 308	3.84	0	Ionic (Protein Cationic)	false
N6	OD1	ASN- 402	3.06	156.17	H-Bond (Ligand Donor)	false
N1	ND2	ASN- 402	3	169.71	H-Bond (Protein Donor)	false
O3G	CA	CA- 901	2.39	0	Metal Acceptor	false
O1B	CA	CA- 901	2.4	0	Metal Acceptor	false
O1A	CA	CA- 901	2.34	0	Metal Acceptor	false