scPDB - 1sb8 entry

Protein Data Bank Entry:

PDB ID : 1sb8

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2004-02-10

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	WbpP
ID:	Q8KN66_PSEAI
AC:	Q8KN66
Organism:	Pseudomonas aeruginosa
Reign:	Bacteria
TaxID:	287
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	20.435
Number of residues:	53
Including
Standard Amino Acids:	46
Non Standard Amino Acids:	1
Water Molecules:	6
Cofactors:	NAD
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.175	732.375

% Hydrophobic	% Polar
34.56	65.44
According to VolSite

Ligand :

HET Code:	UD2
Formula:	C17H25N3O17P2
Molecular weight:	605.338 g/mol
DrugBank ID:	DB02196
Buried Surface Area:	69.99 %
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
39.6819	6.72238	89.9651

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
O6'	N	SER- 103	2.73	154.64	H-Bond (Protein Donor)	false
C1'	CG2	VAL- 104	4.01	0	Hydrophobic	false
O3'	OG	SER- 142	3.4	133.37	H-Bond (Protein Donor)	false
O4'	OG	SER- 142	2.6	139.52	H-Bond (Protein Donor)	false
O3'	OG	SER- 143	3.14	150.53	H-Bond (Protein Donor)	false
C6'	CZ	TYR- 166	3.54	0	Hydrophobic	false
C5'	CE2	TYR- 166	4.03	0	Hydrophobic	false
O4'	OH	TYR- 166	3	161.05	H-Bond (Ligand Donor)	false
N2'	OD1	ASN- 195	3.2	156.9	H-Bond (Ligand Donor)	false
O1B	ND2	ASN- 195	3.17	171.98	H-Bond (Protein Donor)	false
C1B	CG2	VAL- 210	4.35	0	Hydrophobic	false
C4B	CB	VAL- 210	4.42	0	Hydrophobic	false
C5B	CG1	VAL- 210	3.91	0	Hydrophobic	false
O2A	N	VAL- 210	2.8	176.05	H-Bond (Protein Donor)	false
O4	NE1	TRP- 214	3.46	136.2	H-Bond (Protein Donor)	false
N3	O	TYR- 225	2.67	161.36	H-Bond (Ligand Donor)	false
O2	N	ASN- 227	2.79	166.65	H-Bond (Protein Donor)	false
O2'	ND2	ASN- 227	2.99	165.38	H-Bond (Protein Donor)	false
C8'	CD	ARG- 234	3.77	0	Hydrophobic	false
O1B	CZ	ARG- 234	3.31	0	Ionic (Protein Cationic)	false
O1B	NE	ARG- 234	2.74	157.51	H-Bond (Protein Donor)	false
O1B	NH2	ARG- 234	3.03	137.23	H-Bond (Protein Donor)	false
C1B	CD1	LEU- 271	3.78	0	Hydrophobic	false
C4B	CD2	LEU- 271	3.92	0	Hydrophobic	false
O1A	CZ	ARG- 299	3.78	0	Ionic (Protein Cationic)	false
O1A	NH2	ARG- 299	2.91	177.23	H-Bond (Protein Donor)	false
O3B	OD1	ASP- 302	3.19	140.28	H-Bond (Ligand Donor)	false
O3B	OD2	ASP- 302	2.74	151.7	H-Bond (Ligand Donor)	false
C8'	CB	VAL- 303	4.11	0	Hydrophobic	false
C8'	CB	SER- 306	3.58	0	Hydrophobic	false
C4'	C4N	NAD- 342	3.2	0	Hydrophobic	false
O2'	O	HOH- 356	2.97	179.96	H-Bond (Protein Donor)	false
O1A	O	HOH- 381	2.63	153.77	H-Bond (Protein Donor)	false