scPDB - 4o6m entry

Protein Data Bank Entry:

PDB ID : 4o6m

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2013-12-22

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Uncharacterized protein
ID:	O27985_ARCFU
AC:	O27985
Organism:	Archaeoglobus fulgidus
Reign:	Archaea
TaxID:	224325
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	3 %
B	97 %

Ligand binding site composition:

B-Factor:	36.575
Number of residues:	36
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	CA

Cavity properties

Ligandability	Volume (Å3)
1.061	1461.375

% Hydrophobic	% Polar
37.41	62.59
According to VolSite

Ligand :

HET Code:	C5P
Formula:	C9H12N3O8P
Molecular weight:	321.181 g/mol
DrugBank ID:	DB03403
Buried Surface Area:	68.41 %
Polar Surface area:	190.61 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	3
Rings:	2
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
8.56238	38.2807	33.8873

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
O2P	NZ	LYS- 136	3.51	0	Ionic (Protein Cationic)	false
C5'	CD	LYS- 136	4.33	0	Hydrophobic	false
O3P	NH2	ARG- 157	2.9	151.09	H-Bond (Protein Donor)	false
O3P	NH1	ARG- 157	3.04	142.88	H-Bond (Protein Donor)	false
O3P	CZ	ARG- 157	3.4	0	Ionic (Protein Cationic)	false
N4	OD1	ASN- 175	2.81	158.58	H-Bond (Ligand Donor)	false
N4	OG1	THR- 178	2.77	162.89	H-Bond (Ligand Donor)	false
O1P	N	GLY- 218	3.14	122.42	H-Bond (Protein Donor)	false
C1'	CB	ALA- 221	3.98	0	Hydrophobic	false
O3P	CZ	ARG- 222	3.97	0	Ionic (Protein Cationic)	false
O3P	NH2	ARG- 222	3.03	166.93	H-Bond (Protein Donor)	false
O5'	NH1	ARG- 222	3.15	175.54	H-Bond (Protein Donor)	false
O2	N	SER- 228	3.08	159.42	H-Bond (Protein Donor)	false
C2'	CB	ALA- 232	3.61	0	Hydrophobic	false
O1P	CA	CA- 401	2.5	0	Metal Acceptor	false