scPDB - 5a01 entry

Protein Data Bank Entry:

PDB ID : 5a01

Resolution :2.660 Å

Experimental Method : X-ray

Deposition Date : 2015-04-15

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	O-glycosyltransferase
ID:	Q7KJA9_DROME
AC:	Q7KJA9
Organism:	Drosophila melanogaster
Reign:	Eukaryota
TaxID:	7227
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	32.991
Number of residues:	44
Including
Standard Amino Acids:	44
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.188	1400.625

% Hydrophobic	% Polar
37.83	62.17
According to VolSite

Ligand :

HET Code:	12V
Formula:	C17H25N3O16P2S
Molecular weight:	621.403 g/mol
DrugBank ID:	-
Buried Surface Area:	64.88 %
Polar Surface area:	341.76 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:	10

Mass center Coordinates

X	Y	Z
79.2362	-17.4416	-30.9226

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
O7'	NE2	HIS- 537	2.94	158.78	H-Bond (Protein Donor)	false
C4B	CG	PRO- 597	4.05	0	Hydrophobic	false
S5'	CB	PRO- 597	4.26	0	Hydrophobic	false
C6'	CB	PRO- 597	4.24	0	Hydrophobic	false
C6'	CB	THR- 598	4.13	0	Hydrophobic	false
O6'	OG1	THR- 598	2.87	161.88	H-Bond (Ligand Donor)	false
C6'	CD1	LEU- 601	3.83	0	Hydrophobic	false
O4'	O	LEU- 691	2.81	179.2	H-Bond (Ligand Donor)	false
C8'	CG	PRO- 694	3.84	0	Hydrophobic	false
C4'	CZ	PHE- 732	4.49	0	Hydrophobic	false
O2A	NE2	GLN- 869	2.65	154.98	H-Bond (Protein Donor)	false
N3	O	ALA- 926	2.6	156.83	H-Bond (Ligand Donor)	false
O4	N	ALA- 926	2.85	171.06	H-Bond (Protein Donor)	false
O2'	NZ	LYS- 928	2.7	147.12	H-Bond (Protein Donor)	false
C2B	CD	LYS- 928	4.49	0	Hydrophobic	false
C8'	SG	CYS- 947	3.46	0	Hydrophobic	false
C3'	CB	HIS- 950	3.93	0	Hydrophobic	false
O1B	N	THR- 951	2.98	164.82	H-Bond (Protein Donor)	false
O1B	OG1	THR- 951	2.94	177.86	H-Bond (Protein Donor)	false
C3B	CB	THR- 951	4.15	0	Hydrophobic	false
C5'	CG2	THR- 951	3.95	0	Hydrophobic	false
C2B	CG2	THR- 952	4.17	0	Hydrophobic	false
C5B	CG2	THR- 952	4.08	0	Hydrophobic	false
O2'	OD2	ASP- 955	2.65	167.45	H-Bond (Ligand Donor)	false