scPDB - 3hbf entry

Protein Data Bank Entry:

PDB ID : 3hbf

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2009-05-04

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Flavonoid 3-O-glucosyltransferase
ID:	UGFGT_MEDTR
AC:	A6XNC6
Organism:	Medicago truncatula
Reign:	Eukaryota
TaxID:	3880
EC Number:	2.4.1

Chains:

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

Ligand binding site composition:

B-Factor:	33.268
Number of residues:	34
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.571	1822.500

% Hydrophobic	% Polar
49.26	50.74
According to VolSite

Ligand :

HET Code:	MYC
Formula:	C15H8O8
Molecular weight:	316.219 g/mol
DrugBank ID:	DB02375
Buried Surface Area:	65.95 %
Polar Surface area:	153.34 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	1

Mass center Coordinates

X	Y	Z
20.9052	-10.8275	8.13274

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	CD	ARG- 89	3.29	0	Hydrophobic	false
O24	NE2	HIS- 155	2.64	163.46	H-Bond (Protein Donor)	false
C16	CB	PRO- 191	3.87	0	Hydrophobic	false
C5	CG	GLU- 192	4.3	0	Hydrophobic	false
C15	CG	GLU- 192	4.2	0	Hydrophobic	false
O25	O	GLU- 192	3.03	173.42	H-Bond (Ligand Donor)	false
DuAr	DuAr	PHE- 202	3.91	0	Aromatic Face/Face	false
C5	CB	PHE- 202	3.63	0	Hydrophobic	false
C16	CD1	LEU- 206	3.63	0	Hydrophobic	false
C17	CB	ASP- 376	3.88	0	Hydrophobic	false