scPDB - 2ii5 entry

Protein Data Bank Entry:

PDB ID : 2ii5

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2006-09-27

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex, mitochondrial
ID:	ODB2_BOVIN
AC:	P11181
Organism:	Bos taurus
Reign:	Eukaryota
TaxID:	9913
EC Number:	2.3.1.168

Chains:

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

Ligand binding site composition:

B-Factor:	50.584
Number of residues:	31
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.580	573.750

% Hydrophobic	% Polar
43.53	56.47
According to VolSite

Ligand :

HET Code:	CO6
Formula:	C25H38N7O17P3S
Molecular weight:	833.592 g/mol
DrugBank ID:	-
Buried Surface Area:	44.93 %
Polar Surface area:	429.68 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	5
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	21

Mass center Coordinates

X	Y	Z
89.2598	-14.1413	31.111

Binding mode :

What is Poseview ?

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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
O8A	NH2	ARG- 230	2.79	124.44	H-Bond (Protein Donor)	false
O9A	NH2	ARG- 230	3.3	166.68	H-Bond (Protein Donor)	false
O9A	CZ	ARG- 230	3.99	0	Ionic (Protein Cationic)	false
O9A	NZ	LYS- 234	3.77	0	Ionic (Protein Cationic)	false
O8A	NZ	LYS- 243	3.91	0	Ionic (Protein Cationic)	false
C2B	CD2	PHE- 246	4.46	0	Hydrophobic	false
CCP	CG	MET- 247	3.9	0	Hydrophobic	false
CDP	CG2	ILE- 285	3.54	0	Hydrophobic	false
CEP	CG	MET- 287	4.4	0	Hydrophobic	false
CEP	CG	GLN- 317	4.29	0	Hydrophobic	false
N7A	ND2	ASN- 339	3.22	173.62	H-Bond (Protein Donor)	false
O6A	ND2	ASN- 339	3.42	144.19	H-Bond (Protein Donor)	false
CDP	CB	ASN- 339	3.76	0	Hydrophobic	false
CAP	CB	SER- 342	3.86	0	Hydrophobic	false
N6A	O	GLY- 363	2.89	147.78	H-Bond (Ligand Donor)	false
N1A	N	ILE- 365	2.87	169.86	H-Bond (Protein Donor)	false