scPDB - 2iib entry

Protein Data Bank Entry:

PDB ID : 2iib

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2006-09-27

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Alpha-2,3/2,6-sialyltransferase/sialidase
ID:	Q15KI8_PASMD
AC:	Q15KI8
Organism:	Pasteurella multocida
Reign:	Bacteria
TaxID:	747
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	19.509
Number of residues:	36
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.840	546.750

% Hydrophobic	% Polar
33.33	66.67
According to VolSite

Ligand :

HET Code:	C5P
Formula:	C9H12N3O8P
Molecular weight:	321.181 g/mol
DrugBank ID:	DB03403
Buried Surface Area:	72.84 %
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
12.0956	-3.82614	1.40124

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'	CB	SER- 36	4.27	0	Hydrophobic	false
C4'	CB	SER- 36	3.81	0	Hydrophobic	false
C4'	CB	LEU- 37	4.45	0	Hydrophobic	false
N4	O	GLY- 266	3.07	166.65	H-Bond (Ligand Donor)	false
N3	NZ	LYS- 309	3.1	122.5	H-Bond (Protein Donor)	false
O2	NZ	LYS- 309	3.25	140.03	H-Bond (Protein Donor)	false
N4	O	LYS- 309	2.82	143.04	H-Bond (Ligand Donor)	false
O1P	NE2	HIS- 311	2.65	164.12	H-Bond (Protein Donor)	false
C1'	CG	PRO- 312	3.95	0	Hydrophobic	false
O2'	OG	SER- 336	3.17	146.44	H-Bond (Protein Donor)	false
O2	N	PHE- 337	2.72	152.62	H-Bond (Protein Donor)	false
O3P	OG	SER- 355	2.61	164.24	H-Bond (Protein Donor)	false
O5'	OG	SER- 355	3.44	124.63	H-Bond (Protein Donor)	false
O2P	N	SER- 356	2.98	155.31	H-Bond (Protein Donor)	false
O2P	OG	SER- 356	2.58	148.54	H-Bond (Protein Donor)	false
C5'	CB	SER- 356	3.51	0	Hydrophobic	false
C2'	CB	LEU- 357	4.33	0	Hydrophobic	false