scPDB - 2wnb entry

Protein Data Bank Entry:

PDB ID : 2wnb

Resolution :1.550 Å

Experimental Method : X-ray

Deposition Date : 2009-07-08

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	CMP-N-acetylneuraminate-beta-galactosamide-alpha-2,3-sialyltransferase 1
ID:	SIA4A_PIG
AC:	Q02745
Organism:	Sus scrofa
Reign:	Eukaryota
TaxID:	9823
EC Number:	2.4.99.4

Chains:

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

Ligand binding site composition:

B-Factor:	17.077
Number of residues:	32
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	1
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.800	580.500

% Hydrophobic	% Polar
47.09	52.91
According to VolSite

Ligand :

HET Code:	C5P
Formula:	C9H12N3O8P
Molecular weight:	321.181 g/mol
DrugBank ID:	DB03403
Buried Surface Area:	60.62 %
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
23.9269	31.8653	34.2351

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
O1P	ND2	ASN- 150	2.73	151.33	H-Bond (Protein Donor)	false
O4'	N	ASN- 150	3.31	153.74	H-Bond (Protein Donor)	false
C5'	CB	ASN- 150	4.37	0	Hydrophobic	false
C4'	SD	MET- 172	3.25	0	Hydrophobic	false
O3P	ND2	ASN- 173	2.92	123.26	H-Bond (Protein Donor)	false
O1P	ND2	ASN- 173	2.82	156.27	H-Bond (Protein Donor)	false
O3'	N	GLY- 273	2.9	146.3	H-Bond (Protein Donor)	false
C1'	CE2	PHE- 292	4.38	0	Hydrophobic	false
N3	N	GLY- 293	3.3	128.28	H-Bond (Protein Donor)	false
O2	N	GLY- 293	2.91	170.34	H-Bond (Protein Donor)	false
N4	O	GLY- 293	3.36	128.12	H-Bond (Ligand Donor)	false
O2P	NE2	HIS- 302	2.57	160.53	H-Bond (Protein Donor)	false