scPDB - 2y0d entry

Protein Data Bank Entry:

PDB ID : 2y0d

Resolution :2.800 Å

Experimental Method : X-ray

Deposition Date : 2010-12-02

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	UDP-glucose dehydrogenase
ID:	C9E261_BURCE
AC:	C9E261
Organism:	Burkholderia cepacia
Reign:	Bacteria
TaxID:	292
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	5 %
B	95 %

Ligand binding site composition:

B-Factor:	16.902
Number of residues:	43
Including
Standard Amino Acids:	43
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.755	1235.250

% Hydrophobic	% Polar
38.25	61.75
According to VolSite

Ligand :

HET Code:	UGA
Formula:	C15H19N2O18P2
Molecular weight:	577.261 g/mol
DrugBank ID:	DB03041
Buried Surface Area:	73.67 %
Polar Surface area:	336.72 Å2

Number of
H-Bond Acceptors:	18
H-Bond Donors:	6
Rings:	3
Aromatic rings:	0
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
-42.8054	0.461973	14.4065

Binding mode :

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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
O'P	NZ	LYS- 10	3.26	155.8	H-Bond (Protein Donor)	false
O'P	NZ	LYS- 10	3.26	0	Ionic (Protein Cationic)	false
O4'	OE2	GLU- 154	2.85	146.69	H-Bond (Ligand Donor)	false
C3'	CG	LYS- 157	4.08	0	Hydrophobic	false
O1B	N	GLU- 158	3.06	164.65	H-Bond (Protein Donor)	false
O'P	NZ	LYS- 214	3.97	0	Ionic (Protein Cationic)	false
O'Q	NZ	LYS- 214	2.89	0	Ionic (Protein Cationic)	false
O'Q	NZ	LYS- 214	2.89	146.62	H-Bond (Protein Donor)	false
O'Q	ND2	ASN- 218	3.07	158.63	H-Bond (Protein Donor)	false
C1D	CD1	ILE- 225	4.12	0	Hydrophobic	false
O2'	NH1	ARG- 254	3.02	156.71	H-Bond (Protein Donor)	false
O3'	NH2	ARG- 254	3.11	156.64	H-Bond (Protein Donor)	false
N3	O	TYR- 261	3	166.71	H-Bond (Ligand Donor)	false
O4	N	TYR- 261	2.91	144.33	H-Bond (Protein Donor)	false
C4D	CB	TYR- 266	3.77	0	Hydrophobic	false
C1D	CB	TYR- 266	3.92	0	Hydrophobic	false
O3D	N	GLY- 267	2.98	151.96	H-Bond (Protein Donor)	false
C1'	CB	CYS- 270	4.29	0	Hydrophobic	false
C5'	SG	CYS- 270	3.72	0	Hydrophobic	false
C5D	CE2	PHE- 271	4.13	0	Hydrophobic	false
C4D	CD2	PHE- 271	4.43	0	Hydrophobic	false
C1'	CE1	PHE- 271	3.57	0	Hydrophobic	false
C3D	CD2	PHE- 330	3.58	0	Hydrophobic	false
C5D	CE2	PHE- 330	3.66	0	Hydrophobic	false
O1B	NZ	LYS- 331	3.33	161.7	H-Bond (Protein Donor)	false
O2A	NZ	LYS- 331	3.02	155.38	H-Bond (Protein Donor)	false
O1B	NZ	LYS- 331	3.33	0	Ionic (Protein Cationic)	false
O2A	NZ	LYS- 331	3.02	0	Ionic (Protein Cationic)	false
C3D	CB	LYS- 331	3.97	0	Hydrophobic	false
O2	NH1	ARG- 431	3.12	148.19	H-Bond (Protein Donor)	false