scPDB - 4o8j entry

Protein Data Bank Entry:

PDB ID : 4o8j

Resolution :2.040 Å

Experimental Method : X-ray

Deposition Date : 2013-12-27

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	RNA 3'-terminal phosphate cyclase
ID:	RTCA_PYRHO
AC:	O59198
Organism:	Pyrococcus horikoshii
Reign:	Archaea
TaxID:	70601
EC Number:	6.5.1.4

Chains:

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

Ligand binding site composition:

B-Factor:	40.717
Number of residues:	25
Including
Standard Amino Acids:	25
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.259	766.125

% Hydrophobic	% Polar
45.81	54.19
According to VolSite

Ligand :

HET Code:	ADN
Formula:	C10H13N5O4
Molecular weight:	267.241 g/mol
DrugBank ID:	DB00640
Buried Surface Area:	68.9 %
Polar Surface area:	139.54 Å2

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

Mass center Coordinates

X	Y	Z
64.7043	71.9041	69.5868

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
C4'	CD2	LEU- 97	3.71	0	Hydrophobic	false
O3'	NE2	GLN- 100	2.83	152.08	H-Bond (Protein Donor)	false
C1'	CG	PRO- 127	3.58	0	Hydrophobic	false
N6	OD1	ASP- 250	2.75	164.62	H-Bond (Ligand Donor)	false
N1	OD2	ASP- 250	2.81	162.54	H-Bond (Ligand Donor)	false
DuAr	DuAr	PHE- 283	3.74	0	Aromatic Face/Face	false
C2'	CD1	PHE- 283	4.12	0	Hydrophobic	false
O3'	OD1	ASP- 286	2.74	164.04	H-Bond (Ligand Donor)	false
O2'	OD2	ASP- 286	2.78	167.07	H-Bond (Ligand Donor)	false
O2'	NE2	GLN- 287	3.08	159.58	H-Bond (Protein Donor)	false
N3	NE2	GLN- 287	3.43	122.07	H-Bond (Protein Donor)	false