scPDB - 4okk entry

Protein Data Bank Entry:

PDB ID : 4okk

Resolution :2.210 Å

Experimental Method : X-ray

Deposition Date : 2014-01-22

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	3'-5' exoribonuclease MT2234.1
ID:	EXRBN_MYCTO
AC:	P9WJ72
Organism:	Mycobacterium tuberculosis
Reign:	Bacteria
TaxID:	83331
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	10 %
B	90 %

Ligand binding site composition:

B-Factor:	43.662
Number of residues:	22
Including
Standard Amino Acids:	19
Non Standard Amino Acids:	2
Water Molecules:	1
Cofactors:
Metals:	MG MG

Cavity properties

Ligandability	Volume (Å3)
0.367	796.500

% Hydrophobic	% Polar
46.19	53.81
According to VolSite

Ligand :

HET Code:	U5P
Formula:	C9H11N2O9P
Molecular weight:	322.165 g/mol
DrugBank ID:	-
Buried Surface Area:	51.65 %
Polar Surface area:	181.33 Å2

Number of
H-Bond Acceptors:	9
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
15.8652	69.0684	29.1707

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
O3'	OE1	GLU- 8	3.09	153.98	H-Bond (Ligand Donor)	false
C1'	CE1	PHE- 9	4.32	0	Hydrophobic	false
C4'	CZ	PHE- 9	3.59	0	Hydrophobic	false
C5'	CE2	PHE- 9	3.89	0	Hydrophobic	false
O2'	O	PHE- 9	2.58	150.88	H-Bond (Ligand Donor)	false
O3'	N	PHE- 9	2.93	165.55	H-Bond (Protein Donor)	false
C2'	CZ3	TRP- 46	3.88	0	Hydrophobic	false
C2'	CG2	VAL- 47	3.65	0	Hydrophobic	false
C3'	CG2	VAL- 51	4.25	0	Hydrophobic	false
C1'	CE	MET- 106	3.43	0	Hydrophobic	false
O2P	MG	MG- 202	2.76	0	Metal Acceptor	false
O2P	MG	MG- 204	1.82	0	Metal Acceptor	false