scPDB - 3p3c entry

Protein Data Bank Entry:

PDB ID : 3p3c

Resolution :1.250 Å

Experimental Method : X-ray

Deposition Date : 2010-10-04

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_AQUAE
AC:	O67648
Organism:	Aquifex aeolicus
Reign:	Bacteria
TaxID:	224324
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	9.885
Number of residues:	37
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.464	951.750

% Hydrophobic	% Polar
43.97	56.03
According to VolSite

Ligand :

HET Code:	3P3
Formula:	C21H18N2O4
Molecular weight:	362.379 g/mol
DrugBank ID:	-
Buried Surface Area:	62.66 %
Polar Surface area:	98.66 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	4
Rings:	2
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
-12.4542	17.0539	-15.7786

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
C11	CD1	ILE- 18	3.39	0	Hydrophobic	false
O01	OG1	THR- 179	2.67	135.45	H-Bond (Protein Donor)	false
N06	OG1	THR- 179	3.06	160.34	H-Bond (Ligand Donor)	false
C10	CG2	THR- 179	4.42	0	Hydrophobic	false
C26	CB	THR- 179	4.47	0	Hydrophobic	false
C26	CE2	PHE- 180	3.67	0	Hydrophobic	false
C12	CB	ALA- 181	3.85	0	Hydrophobic	false
C15	CB	ALA- 181	3.93	0	Hydrophobic	false
C24	CG2	ILE- 186	4.44	0	Hydrophobic	false
C18	CD1	ILE- 186	3.8	0	Hydrophobic	false
C14	CD1	ILE- 189	3.62	0	Hydrophobic	false
C20	CD2	LEU- 200	4.3	0	Hydrophobic	false
C21	CG	LEU- 200	4.07	0	Hydrophobic	false
C15	CG2	THR- 203	3.8	0	Hydrophobic	false
C18	CG2	VAL- 205	4.44	0	Hydrophobic	false
C20	CG2	VAL- 205	4.06	0	Hydrophobic	false
O27	OD2	ASP- 230	2.99	151.56	H-Bond (Ligand Donor)	false
N03	NE2	HIS- 253	2.67	121.69	H-Bond (Ligand Donor)	false
O01	ZN	ZN- 401	2.06	0	Metal Acceptor	false
O04	ZN	ZN- 401	2.09	0	Metal Acceptor	false