scPDB - 3e8s entry

Protein Data Bank Entry:

PDB ID : 3e8s

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2008-08-20

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Uncharacterized protein
ID:	Q88JU2_PSEPK
AC:	Q88JU2
Organism:	Pseudomonas putida
Reign:	Bacteria
TaxID:	160488
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	42.242
Number of residues:	41
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	0
Water Molecules:	6
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.006	705.375

% Hydrophobic	% Polar
55.02	44.98
According to VolSite

Ligand :

HET Code:	SAH
Formula:	C14H20N6O5S
Molecular weight:	384.411 g/mol
DrugBank ID:	DB01752
Buried Surface Area:	76.55 %
Polar Surface area:	212.38 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
69.4587	23.2807	9.37504

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
SD	CH2	TRP- 16	3.41	0	Hydrophobic	false
C5'	CZ2	TRP- 16	3.59	0	Hydrophobic	false
C4'	CE2	TRP- 16	4.49	0	Hydrophobic	false
C2'	CD2	TRP- 16	3.83	0	Hydrophobic	false
SD	CZ2	TRP- 23	3.66	0	Hydrophobic	false
CG	CZ2	TRP- 23	3.91	0	Hydrophobic	false
O	NH2	ARG- 35	3.42	130.38	H-Bond (Protein Donor)	false
O	NH1	ARG- 35	2.94	149.33	H-Bond (Protein Donor)	false
OXT	NH2	ARG- 35	3.1	140.75	H-Bond (Protein Donor)	false
OXT	NH1	ARG- 35	3.23	136.08	H-Bond (Protein Donor)	false
O	CZ	ARG- 35	3.6	0	Ionic (Protein Cationic)	false
OXT	CZ	ARG- 35	3.56	0	Ionic (Protein Cationic)	false
N	O	GLY- 59	2.66	161.18	H-Bond (Ligand Donor)	false
OXT	NE1	TRP- 64	3.08	166.8	H-Bond (Protein Donor)	false
O3'	OD2	ASP- 80	2.6	159.47	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 80	2.71	160.64	H-Bond (Ligand Donor)	false
N3	N	GLY- 81	3.13	131.75	H-Bond (Protein Donor)	false
C3'	CD1	LEU- 85	3.84	0	Hydrophobic	false
N1	N	TYR- 102	2.96	157.19	H-Bond (Protein Donor)	false
DuAr	DuAr	TYR- 102	3.51	0	Aromatic Face/Face	false
N	O	ASN- 122	2.86	161.77	H-Bond (Ligand Donor)	false
OXT	ND2	ASN- 122	2.87	159.15	H-Bond (Protein Donor)	false
C5'	CD1	LEU- 126	4.32	0	Hydrophobic	false
N	O	HOH- 302	2.78	154.87	H-Bond (Ligand Donor)	false
O	O	HOH- 307	2.62	179.97	H-Bond (Protein Donor)	false