scPDB - 3ruh entry

Protein Data Bank Entry:

PDB ID : 3ruh

Resolution :2.880 Å

Experimental Method : X-ray

Deposition Date : 2011-05-05

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	UDP-N-acetylglucosamine 4-epimerase
ID:	GNE_PLESH
AC:	Q7BJX9
Organism:	Plesiomonas shigelloides
Reign:	Bacteria
TaxID:	703
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	37.495
Number of residues:	48
Including
Standard Amino Acids:	47
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:	NAD
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.764	1073.250

% Hydrophobic	% Polar
37.11	62.89
According to VolSite

Ligand :

HET Code:	UD6
Formula:	C18H26N2O17P2
Molecular weight:	604.350 g/mol
DrugBank ID:	-
Buried Surface Area:	69.54 %
Polar Surface area:	313.66 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	6
Rings:	3
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
-21.0407	-16.2848	47.1445

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
O6'	N	SER- 103	3.1	169.05	H-Bond (Protein Donor)	false
O3'	OG	SER- 142	3.3	132.7	H-Bond (Protein Donor)	false
O4'	OG	SER- 142	3.36	143.48	H-Bond (Protein Donor)	false
O3'	OG	SER- 143	3.12	156.73	H-Bond (Ligand Donor)	false
C8'	CB	SER- 143	4.21	0	Hydrophobic	false
C2'	CB	SER- 144	4.35	0	Hydrophobic	false
C4'	CE2	TYR- 166	4.45	0	Hydrophobic	false
O1B	ND2	ASN- 195	3.23	144.44	H-Bond (Protein Donor)	false
C1B	CG2	VAL- 210	4.41	0	Hydrophobic	false
C4B	CB	VAL- 210	4.49	0	Hydrophobic	false
C5B	CG1	VAL- 210	4	0	Hydrophobic	false
O2A	N	VAL- 210	3.36	172.24	H-Bond (Protein Donor)	false
O4	NZ	LYS- 213	2.65	161.88	H-Bond (Protein Donor)	false
O2	N	ASN- 227	2.73	168.51	H-Bond (Protein Donor)	false
O2'	ND2	ASN- 227	2.97	144.96	H-Bond (Protein Donor)	false
C2B	CB	ASN- 227	4.29	0	Hydrophobic	false
O1B	NE	ARG- 234	2.91	145.79	H-Bond (Protein Donor)	false
O1B	NH2	ARG- 234	2.87	145.42	H-Bond (Protein Donor)	false
O1B	CZ	ARG- 234	3.32	0	Ionic (Protein Cationic)	false
C5B	CD	ARG- 234	4.32	0	Hydrophobic	false
C1B	CD1	LEU- 271	3.67	0	Hydrophobic	false
C3B	CD1	LEU- 271	4.44	0	Hydrophobic	false
C4B	CD2	LEU- 271	3.78	0	Hydrophobic	false
O3B	OD1	ASP- 302	3.09	157.7	H-Bond (Ligand Donor)	false
C8'	CB	VAL- 303	4.24	0	Hydrophobic	false
C8'	CB	SER- 306	3.79	0	Hydrophobic	false
C3'	C4N	NAD- 343	3.41	0	Hydrophobic	false
C4'	C4N	NAD- 343	3.8	0	Hydrophobic	false