scPDB - 3o3n entry

Protein Data Bank Entry:

PDB ID : 3o3n

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2010-07-25

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	(R)-2-hydroxyisocaproyl-CoA dehydratase alpha subunit
ID:	HADB_PEPDI
AC:	Q5U924
Organism:	Peptoclostridium difficile
Reign:	Bacteria
TaxID:	1496
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	35.302
Number of residues:	49
Including
Standard Amino Acids:	47
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.403	1366.875

% Hydrophobic	% Polar
55.31	44.69
According to VolSite

Ligand :

HET Code:	IRC
Formula:	C27H42N7O18P3S
Molecular weight:	877.645 g/mol
DrugBank ID:	-
Buried Surface Area:	47.56 %
Polar Surface area:	449.91 Å2

Number of
H-Bond Acceptors:	23
H-Bond Donors:	6
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	23

Mass center Coordinates

X	Y	Z
51.2611	8.53354	0.695643

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
CCP	CD1	LEU- 15	4.03	0	Hydrophobic	false
CI6	CB	SER- 37	4.07	0	Hydrophobic	false
CI6	CG2	VAL- 38	3.62	0	Hydrophobic	false
C2P	CB	GLU- 55	4.29	0	Hydrophobic	false
O5P	ND2	ASN- 56	3.33	154.9	H-Bond (Protein Donor)	false
C6P	CB	ASN- 56	4.28	0	Hydrophobic	false
C6P	CB	ALA- 59	4.19	0	Hydrophobic	false
C2P	CE2	TYR- 86	3.67	0	Hydrophobic	false
CEP	CD2	LEU- 102	4.35	0	Hydrophobic	false
CI3	CG2	ILE- 116	4.06	0	Hydrophobic	false
CI6	CG2	ILE- 116	3.75	0	Hydrophobic	false
C2P	CE	MET- 218	4.43	0	Hydrophobic	false
C6P	CE	MET- 218	3.62	0	Hydrophobic	false
C6P	CB	ALA- 219	4.39	0	Hydrophobic	false
CAP	CB	ALA- 219	3.63	0	Hydrophobic	false
CCP	CB	ALA- 219	4.11	0	Hydrophobic	false
S1P	CD1	ILE- 265	3.86	0	Hydrophobic	false
CI2	CD1	ILE- 265	3.94	0	Hydrophobic	false
CI5	CE1	TYR- 290	3.66	0	Hydrophobic	false
CI5	CB	ALA- 293	4.42	0	Hydrophobic	false
CI6	CZ2	TRP- 294	3.43	0	Hydrophobic	false
CI4	CH2	TRP- 294	4.03	0	Hydrophobic	false
CI5	CE	MET- 313	3.59	0	Hydrophobic	false
CI5	CZ	PHE- 314	3.81	0	Hydrophobic	false