scPDB - 2acw entry

Protein Data Bank Entry:

PDB ID : 2acw

Resolution :2.600 Å

Experimental Method : X-ray

Deposition Date : 2005-07-19

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Glycosyltransferase
ID:	Q5IFH7_MEDTR
AC:	Q5IFH7
Organism:	Medicago truncatula
Reign:	Eukaryota
TaxID:	3880
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	49.119
Number of residues:	40
Including
Standard Amino Acids:	40
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.403	1090.125

% Hydrophobic	% Polar
65.94	34.06
According to VolSite

Ligand :

HET Code:	UPG
Formula:	C15H22N2O17P2
Molecular weight:	564.286 g/mol
DrugBank ID:	DB01861
Buried Surface Area:	75.91 %
Polar Surface area:	316.82 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	7
Rings:	3
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
4.47158	28.0138	-8.4495

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
C4C	CG2	ILE- 20	3.9	0	Hydrophobic	false
C6'	CB	THR- 143	4.43	0	Hydrophobic	false
O6'	OG1	THR- 143	3.46	157.66	H-Bond (Ligand Donor)	false
O1B	OG	SER- 285	3.49	126.07	H-Bond (Protein Donor)	false
O2B	OG	SER- 285	3.36	158.93	H-Bond (Protein Donor)	false
O2B	N	SER- 285	3.28	143.53	H-Bond (Protein Donor)	false
C1'	CE	MET- 286	3.78	0	Hydrophobic	false
C1C	CH2	TRP- 339	4.21	0	Hydrophobic	false
N3	O	ALA- 340	2.8	147.13	H-Bond (Ligand Donor)	false
O4	N	ALA- 340	3.31	157.4	H-Bond (Protein Donor)	false
C2C	CB	GLN- 342	3.87	0	Hydrophobic	false
C6'	CB	TRP- 360	4.41	0	Hydrophobic	false
O4'	N	TRP- 360	2.62	172.49	H-Bond (Protein Donor)	false
O1A	N	ASN- 361	3.17	145.06	H-Bond (Protein Donor)	false
O1A	ND2	ASN- 361	3.23	150.71	H-Bond (Protein Donor)	false
C3C	CB	ASN- 361	4.03	0	Hydrophobic	false
O2A	N	SER- 362	2.92	150.74	H-Bond (Protein Donor)	false
O2C	OE2	GLU- 365	3.03	151.58	H-Bond (Ligand Donor)	false
O2C	OE1	GLU- 365	2.71	142.11	H-Bond (Ligand Donor)	false
O3C	OE2	GLU- 365	2.64	164.63	H-Bond (Ligand Donor)	false
C2'	CE2	TYR- 379	4.4	0	Hydrophobic	false
O3'	OE1	GLU- 381	2.97	169.98	H-Bond (Ligand Donor)	false
O4'	OE1	GLU- 381	2.56	152.15	H-Bond (Ligand Donor)	false
C3'	CG	GLN- 382	4.28	0	Hydrophobic	false
O2'	NE2	GLN- 382	2.91	121.27	H-Bond (Protein Donor)	false