scPDB - 3vrb entry

Protein Data Bank Entry:

PDB ID : 3vrb

Resolution :2.910 Å

Experimental Method : X-ray

Deposition Date : 2012-04-07

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial	Cytochrome b-large subunit
ID:	O44074_ASCSU	P92506_ASCSU
AC:	O44074	P92506
Organism:	Ascaris suum
Reign:	Eukaryota
TaxID:	6253
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
F	48 %
G	44 %
H	8 %

Ligand binding site composition:

B-Factor:	68.413
Number of residues:	31
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.036	1272.375

% Hydrophobic	% Polar
51.72	48.28
According to VolSite

Ligand :

HET Code:	FTN
Formula:	C17H16F3NO2
Molecular weight:	323.310 g/mol
DrugBank ID:	-
Buried Surface Area:	63.84 %
Polar Surface area:	38.33 Å2

Number of
H-Bond Acceptors:	2
H-Bond Donors:	1
Rings:	2
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
2.69957	15.3091	19.455

Binding mode :

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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
C17	CB	LEU- 60	3.96	0	Hydrophobic	false
C16	CB	TYR- 63	4.23	0	Hydrophobic	false
C11	CE3	TRP- 69	4.17	0	Hydrophobic	false
C17	CH2	TRP- 69	3.6	0	Hydrophobic	false
C15	CD2	TRP- 69	3.27	0	Hydrophobic	false
C5	CB	SER- 72	4.34	0	Hydrophobic	false
C3	CD	ARG- 76	4.38	0	Hydrophobic	false
C5	CG	ARG- 76	3.44	0	Hydrophobic	false
C6	CD	ARG- 76	3.93	0	Hydrophobic	false
DuAr	CZ	ARG- 76	3.57	28.75	Pi/Cation	false
F1	CB	ASP- 106	3.99	0	Hydrophobic	false
F3	CB	ASP- 106	3.92	0	Hydrophobic	false
C1	CZ	TYR- 107	4.15	0	Hydrophobic	false
F1	CE2	TYR- 107	3.32	0	Hydrophobic	false
C14	CE2	TYR- 107	4.19	0	Hydrophobic	false
O1	OH	TYR- 107	2.87	131.51	H-Bond (Protein Donor)	false
F2	CB	PRO- 193	3.51	0	Hydrophobic	false
C16	CG	PRO- 193	4.48	0	Hydrophobic	false
F2	CB	SER- 194	4.25	0	Hydrophobic	false
C16	CH2	TRP- 196	3.75	0	Hydrophobic	false
O1	NE1	TRP- 197	2.96	160.76	H-Bond (Protein Donor)	false
C14	CZ2	TRP- 197	3.86	0	Hydrophobic	false
C7	CB	HIS- 240	3.58	0	Hydrophobic	false
F2	CD1	ILE- 242	3.9	0	Hydrophobic	false
C2	CD1	ILE- 242	4.35	0	Hydrophobic	false