scPDB - 4j3d entry

Protein Data Bank Entry:

PDB ID : 4j3d

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2013-02-05

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
B	100 %

Ligand binding site composition:

B-Factor:	33.958
Number of residues:	37
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	2
Water Molecules:	0
Cofactors:
Metals:	ZN ZN

Cavity properties

Ligandability	Volume (Å3)
0.884	729.000

% Hydrophobic	% Polar
52.31	47.69
According to VolSite

Ligand :

HET Code:	1JS
Formula:	C23H25N3O5
Molecular weight:	423.462 g/mol
DrugBank ID:	-
Buried Surface Area:	69.37 %
Polar Surface area:	127.76 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	5
Rings:	2
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
-3.66923	-9.8269	-18.0773

Binding mode :

What is Poseview ?

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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
C12	CD2	LEU- 18	3.98	0	Hydrophobic	false
C9	CD1	LEU- 18	4.14	0	Hydrophobic	false
N17	OG1	THR- 190	2.69	149.53	H-Bond (Ligand Donor)	false
O30	OG1	THR- 190	2.71	159.09	H-Bond (Protein Donor)	false
C13	CG2	THR- 190	3.8	0	Hydrophobic	false
C20	CE2	PHE- 191	4.46	0	Hydrophobic	false
C21	CZ	PHE- 191	3.76	0	Hydrophobic	false
C27	CB	ASP- 196	3.33	0	Hydrophobic	false
O28	OD2	ASP- 196	2.63	164.6	H-Bond (Ligand Donor)	false
C9	CG1	ILE- 197	4.33	0	Hydrophobic	false
C5	CD1	ILE- 197	3.98	0	Hydrophobic	false
C7	CG1	ILE- 197	3.63	0	Hydrophobic	false
C3	CG2	ILE- 197	3.35	0	Hydrophobic	false
C10	CD2	LEU- 200	3.44	0	Hydrophobic	false
C27	CD2	LEU- 200	4.09	0	Hydrophobic	false
C10	CB	ALA- 206	3.81	0	Hydrophobic	false
C8	CB	ALA- 206	4.28	0	Hydrophobic	false
C14	CB	ALA- 214	4.02	0	Hydrophobic	false
C5	CB	ALA- 214	4.3	0	Hydrophobic	false
C8	CB	ALA- 214	4.33	0	Hydrophobic	false
C5	CG2	VAL- 216	3.36	0	Hydrophobic	false
O23	NZ	LYS- 238	2.69	144.05	H-Bond (Protein Donor)	false
O30	ZN	ZN- 301	2.09	0	Metal Acceptor	false
O32	ZN	ZN- 301	2.39	0	Metal Acceptor	false
O32	ZN	ZN- 302	2.77	0	Metal Acceptor	false