scPDB - 3bxo entry

Protein Data Bank Entry:

PDB ID : 3bxo

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2008-01-14

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	dTDP-3-amino-3,4,6-trideoxy-alpha-D-glucopyranose
ID:	DESVI_STRVZ
AC:	Q9ZGH6
Organism:	Streptomyces venezuelae
Reign:	Bacteria
TaxID:	54571
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	11.239
Number of residues:	35
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.906	864.000

% Hydrophobic	% Polar
50.39	49.61
According to VolSite

Ligand :

HET Code:	UPP
Formula:	C15H16N2O12P2
Molecular weight:	478.241 g/mol
DrugBank ID:	DB02790
Buried Surface Area:	71.45 %
Polar Surface area:	226.67 Å2

Number of
H-Bond Acceptors:	12
H-Bond Donors:	3
Rings:	3
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
8.84081	0.469806	56.4909

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
O1B	OH	TYR- 14	2.86	155.49	H-Bond (Protein Donor)	false
O3B	OH	TYR- 14	3.37	133.65	H-Bond (Protein Donor)	false
O2A	NH2	ARG- 17	2.85	150.53	H-Bond (Protein Donor)	false
O2A	NH1	ARG- 17	3.43	128.4	H-Bond (Protein Donor)	false
O1B	NH1	ARG- 17	2.63	138.04	H-Bond (Protein Donor)	false
O2A	CZ	ARG- 17	3.56	0	Ionic (Protein Cationic)	false
O1B	CZ	ARG- 17	3.63	0	Ionic (Protein Cationic)	false
C2'	CZ	PHE- 106	3.29	0	Hydrophobic	false
C4'	CB	SER- 107	4.02	0	Hydrophobic	false
C4B	CH2	TRP- 140	4	0	Hydrophobic	false
C1B	CE2	TRP- 141	3.79	0	Hydrophobic	false
N3	O	THR- 145	2.8	171.56	H-Bond (Ligand Donor)	false
C2B	CE1	PHE- 146	4.24	0	Hydrophobic	false
O2	N	ALA- 147	2.82	146.09	H-Bond (Protein Donor)	false
O2'	O	ALA- 147	2.87	139.32	H-Bond (Ligand Donor)	false
C5B	CE2	TRP- 150	4.47	0	Hydrophobic	false
C2B	CB	TRP- 150	3.38	0	Hydrophobic	false
O2A	OG	SER- 152	3.07	159.16	H-Bond (Protein Donor)	false
O1A	CZ	ARG- 165	3.21	0	Ionic (Protein Cationic)	false
O1B	CZ	ARG- 165	3.67	0	Ionic (Protein Cationic)	false
O1A	NH2	ARG- 165	2.76	146.13	H-Bond (Protein Donor)	false
O1A	NH1	ARG- 165	2.83	141.1	H-Bond (Protein Donor)	false
O1A	OG	SER- 167	2.65	171.83	H-Bond (Protein Donor)	false
C3B	CB	SER- 169	4	0	Hydrophobic	false
O3'	OG	SER- 169	2.65	163.27	H-Bond (Ligand Donor)	false
C3B	CE	MET- 178	3.88	0	Hydrophobic	false
C6'	CE	MET- 178	3.75	0	Hydrophobic	false
C5'	CD1	ILE- 200	4.11	0	Hydrophobic	false
O2B	CZ	ARG- 229	3.79	0	Ionic (Protein Cationic)	false
O2B	NH2	ARG- 229	2.84	152.54	H-Bond (Protein Donor)	false