scPDB - 3u1y entry

Protein Data Bank Entry:

PDB ID : 3u1y

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2011-09-30

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	UDP-3-O-acyl-N-acetylglucosamine deacetylase
ID:	LPXC_PSEAE
AC:	P47205
Organism:	Pseudomonas aeruginosa
Reign:	Bacteria
TaxID:	208964
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	91 %
B	9 %

Ligand binding site composition:

B-Factor:	28.892
Number of residues:	46
Including
Standard Amino Acids:	45
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.934	1650.375

% Hydrophobic	% Polar
52.97	47.03
According to VolSite

Ligand :

HET Code:	03I
Formula:	C25H35N2O6S
Molecular weight:	491.620 g/mol
DrugBank ID:	-
Buried Surface Area:	61.04 %
Polar Surface area:	114.75 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
14.5738	5.45774	25.5092

Binding mode :

What is Poseview ?

2D View
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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
C13	CD1	LEU- 18	4.26	0	Hydrophobic	false
C11	CD2	LEU- 18	3.82	0	Hydrophobic	false
C22	CG	MET- 62	3.78	0	Hydrophobic	false
C10	CE	MET- 62	3.75	0	Hydrophobic	false
O24	OG1	THR- 190	2.59	157.76	H-Bond (Protein Donor)	false
C12	CG2	THR- 190	3.96	0	Hydrophobic	false
C19	CE1	PHE- 191	3.52	0	Hydrophobic	false
C26	CG	MET- 194	4.34	0	Hydrophobic	false
C31	SD	MET- 194	4	0	Hydrophobic	false
C26	CG1	ILE- 197	3.76	0	Hydrophobic	false
C4	CD1	ILE- 197	3.8	0	Hydrophobic	false
C9	CD1	LEU- 200	3.91	0	Hydrophobic	false
C2	CD1	LEU- 200	3.87	0	Hydrophobic	false
C1	CB	ALA- 206	3.91	0	Hydrophobic	false
C6	CB	ALA- 214	4.11	0	Hydrophobic	false
C13	CB	ALA- 214	4.01	0	Hydrophobic	false
C4	CG1	VAL- 216	4.07	0	Hydrophobic	false
C5	CG2	VAL- 216	3.89	0	Hydrophobic	false
C25	CG1	VAL- 216	4.09	0	Hydrophobic	false
C31	CD1	LEU- 223	4.19	0	Hydrophobic	false
C19	CD	LYS- 238	4.34	0	Hydrophobic	false
O20	NZ	LYS- 238	3.26	148.72	H-Bond (Protein Donor)	false
O24	ZN	ZN- 400	2.19	0	Metal Acceptor	false
O28	ZN	ZN- 400	2.13	0	Metal Acceptor	false