scPDB - 2vig entry

Protein Data Bank Entry:

PDB ID : 2vig

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2007-11-30

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Short-chain specific acyl-CoA dehydrogenase, mitochondrial
ID:	ACADS_HUMAN
AC:	P16219
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	1.3.8.1

Chains:

Chain Name:	Percentage of Residues within binding site
G	97 %
H	3 %

Ligand binding site composition:

B-Factor:	29.352
Number of residues:	39
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	1
Water Molecules:	6
Cofactors:	FAD
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.002	465.750

% Hydrophobic	% Polar
52.90	47.10
According to VolSite

Ligand :

HET Code:	COS
Formula:	C21H32N7O16P3S2
Molecular weight:	795.567 g/mol
DrugBank ID:	DB04036
Buried Surface Area:	47.46 %
Polar Surface area:	451.41 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	6
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	19

Mass center Coordinates

X	Y	Z
-9.62324	-8.03559	79.8267

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
S1P	CE2	PHE- 152	3.87	0	Hydrophobic	false
C2P	CD2	LEU- 154	3.98	0	Hydrophobic	false
N8P	O	SER- 161	3.24	160.38	H-Bond (Ligand Donor)	false
CEP	CB	ALA- 163	3.61	0	Hydrophobic	false
C5B	CB	ASN- 207	4.48	0	Hydrophobic	false
O3A	ND2	ASN- 207	3	122.64	H-Bond (Protein Donor)	false
O5A	ND2	ASN- 207	2.71	150.37	H-Bond (Protein Donor)	false
CCP	CZ	PHE- 261	3.98	0	Hydrophobic	false
CEP	CZ	PHE- 261	4.01	0	Hydrophobic	false
C5B	CE2	PHE- 261	3.69	0	Hydrophobic	false
CEP	CE	MET- 265	4.16	0	Hydrophobic	false
C2P	CD2	LEU- 268	3.57	0	Hydrophobic	false
N6A	OD2	ASP- 269	2.81	160.97	H-Bond (Ligand Donor)	false
O9P	NH2	ARG- 272	3.47	148.79	H-Bond (Protein Donor)	false
O5P	NH2	ARG- 272	3.15	148.81	H-Bond (Protein Donor)	false
CDP	CZ	PHE- 300	3.37	0	Hydrophobic	false
S'P	CB	TYR- 391	3.77	0	Hydrophobic	false
S1P	CG	GLU- 392	4.24	0	Hydrophobic	false
S'P	CG	GLU- 392	3.68	0	Hydrophobic	false
CDP	CD1	ILE- 397	4.43	0	Hydrophobic	false
CAP	CG2	ILE- 397	4.02	0	Hydrophobic	false
S'P	C2'	FAD- 600	3.67	0	Hydrophobic	false
N4P	O	HOH- 2037	2.91	146.41	H-Bond (Ligand Donor)	false
N6A	O	HOH- 2078	2.88	122.66	H-Bond (Ligand Donor)	false
OAP	O	HOH- 2129	3.41	167.19	H-Bond (Ligand Donor)	false
O5A	O	HOH- 2130	2.71	138.46	H-Bond (Protein Donor)	false