scPDB - 5dep entry

Protein Data Bank Entry:

PDB ID : 5dep

Resolution :2.160 Å

Experimental Method : X-ray

Deposition Date : 2015-08-25

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
ID:	LPXA_PSEA7
AC:	A6V1E4
Organism:	Pseudomonas aeruginosa
Reign:	Bacteria
TaxID:	381754
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	58 %
B	42 %

Ligand binding site composition:

B-Factor:	32.314
Number of residues:	39
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.099	1218.375

% Hydrophobic	% Polar
49.31	50.69
According to VolSite

Ligand :

HET Code:	UD1
Formula:	C17H25N3O17P2
Molecular weight:	605.338 g/mol
DrugBank ID:	DB03397
Buried Surface Area:	51.66 %
Polar Surface area:	325.69 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	7
Rings:	3
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
25.4437	-7.25382	34.0726

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
C3'	CB	ASP- 70	4.22	0	Hydrophobic	false
C8'	CD1	LEU- 71	4.08	0	Hydrophobic	false
O7'	N	LEU- 71	2.9	171.19	H-Bond (Protein Donor)	false
O5'	NZ	LYS- 72	3.3	124.36	H-Bond (Protein Donor)	false
O6'	NZ	LYS- 72	2.66	142.44	H-Bond (Protein Donor)	false
C8'	CD2	LEU- 112	4.41	0	Hydrophobic	false
C8'	CE	MET- 114	3.96	0	Hydrophobic	false
O3'	NE2	HIS- 121	3.36	168.21	H-Bond (Ligand Donor)	false
O4'	NE2	HIS- 121	2.97	149.33	H-Bond (Ligand Donor)	false
C8'	CD1	ILE- 130	3.66	0	Hydrophobic	false
O6'	NE2	HIS- 140	2.97	167.03	H-Bond (Protein Donor)	false
O3B	NE2	HIS- 156	3.13	171.12	H-Bond (Ligand Donor)	false
O1A	NE2	GLN- 157	3.17	178	H-Bond (Protein Donor)	false
C6'	CE2	TYR- 158	3.95	0	Hydrophobic	false
O6'	OH	TYR- 158	3.49	130.74	H-Bond (Ligand Donor)	false
C2B	CZ	PHE- 166	4.05	0	Hydrophobic	false
N3	OD1	ASN- 194	2.65	164.36	H-Bond (Ligand Donor)	false
O4	ND2	ASN- 194	3.2	152.69	H-Bond (Protein Donor)	false
O5B	NH2	ARG- 200	3.26	143.4	H-Bond (Protein Donor)	false
O1B	NH1	ARG- 200	2.72	175.18	H-Bond (Protein Donor)	false
O1B	CZ	ARG- 200	3.59	0	Ionic (Protein Cationic)	false