scPDB - 2de4 entry

Protein Data Bank Entry:

PDB ID : 2de4

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2006-02-08

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	2'-hydroxybiphenyl-2-sulfinate desulfinase
ID:	SOXB_RHOSG
AC:	P54997
Organism:	Rhodococcus sp.
Reign:	Bacteria
TaxID:	54064
EC Number:	3.13.1.3

Chains:

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

Ligand binding site composition:

B-Factor:	9.120
Number of residues:	30
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.613	253.125

% Hydrophobic	% Polar
80.00	20.00
According to VolSite

Ligand :

HET Code:	BPS
Formula:	C12H9O2S
Molecular weight:	217.264 g/mol
DrugBank ID:	DB07483
Buried Surface Area:	75.79 %
Polar Surface area:	59.34 Å2

Number of
H-Bond Acceptors:	2
H-Bond Donors:	0
Rings:	2
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	2

Mass center Coordinates

X	Y	Z
-1.3564	2.9114	40.5644

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
OX1	OG	SER- 27	2.7	154.38	H-Bond (Protein Donor)	false
CX4	CB	SER- 27	3.8	0	Hydrophobic	false
CX6	CG	PRO- 28	4.03	0	Hydrophobic	false
OX1	NE2	HIS- 60	2.7	144.22	H-Bond (Protein Donor)	false
OX1	CZ	ARG- 70	3.88	0	Ionic (Protein Cationic)	false
OX1	NH2	ARG- 70	2.73	129.26	H-Bond (Protein Donor)	false
CX8	CD1	LEU- 152	3.79	0	Hydrophobic	false
CX9	CG2	VAL- 186	4.09	0	Hydrophobic	false
CXB	CD2	LEU- 202	3.87	0	Hydrophobic	false
CX6	CD1	LEU- 226	3.58	0	Hydrophobic	false