scPDB - 5ahs entry

Protein Data Bank Entry:

PDB ID : 5ahs

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2015-02-06

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Acyl-CoA dehydrogenase
ID:	K4L7X3_9BURK
AC:	K4L7X3
Organism:	Advenella mimigardefordensis DPN7
Reign:	Bacteria
TaxID:	1247726
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
C	3 %
D	97 %

Ligand binding site composition:

B-Factor:	52.177
Number of residues:	39
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	1
Water Molecules:	3
Cofactors:	FAD
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.957	671.625

% Hydrophobic	% Polar
41.71	58.29
According to VolSite

Ligand :

HET Code:	COA
Formula:	C21H32N7O16P3S
Molecular weight:	763.502 g/mol
DrugBank ID:	DB01992
Buried Surface Area:	46.37 %
Polar Surface area:	426.11 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	6
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	18

Mass center Coordinates

X	Y	Z
33.3901	33.4969	8.97171

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
C2P	CB	ILE- 123	4.27	0	Hydrophobic	false
N8P	O	SER- 130	2.79	164.5	H-Bond (Ligand Donor)	false
CEP	CB	ALA- 132	4.33	0	Hydrophobic	false
C6P	CB	ALA- 132	4.03	0	Hydrophobic	false
C5B	CE2	PHE- 236	4.47	0	Hydrophobic	false
C1B	CB	ALA- 237	3.62	0	Hydrophobic	false
C4B	CB	ALA- 237	4.3	0	Hydrophobic	false
C6P	CE	MET- 240	4.14	0	Hydrophobic	false
S1P	CZ	TYR- 243	3.51	0	Hydrophobic	false
N1A	ND2	ASN- 244	3.12	137.21	H-Bond (Protein Donor)	false
N6A	OD1	ASN- 244	2.88	152.84	H-Bond (Ligand Donor)	false
O5P	NH2	ARG- 247	3.02	143.67	H-Bond (Protein Donor)	false
CAP	CG2	ILE- 371	3.82	0	Hydrophobic	false
S1P	C2'	FAD- 410	4.01	0	Hydrophobic	false
N4P	O	HOH- 2092	3.05	149.98	H-Bond (Ligand Donor)	false