scPDB - 5dw5 entry

Protein Data Bank Entry:

PDB ID : 5dw5

Resolution :1.660 Å

Experimental Method : X-ray

Deposition Date : 2015-09-22

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Succinyl-CoA:acetate CoA-transferase
ID:	SCACT_ACEAC
AC:	B3EY95
Organism:	Acetobacter aceti
Reign:	Bacteria
TaxID:	435
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	19.640
Number of residues:	53
Including
Standard Amino Acids:	46
Non Standard Amino Acids:	0
Water Molecules:	7
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.369	381.375

% Hydrophobic	% Polar
33.63	66.37
According to VolSite

Ligand :

HET Code:	0T1
Formula:	C22H34N7O16P3
Molecular weight:	745.464 g/mol
DrugBank ID:	-
Buried Surface Area:	45.57 %
Polar Surface area:	387.31 Å2

Number of
H-Bond Acceptors:	20
H-Bond Donors:	5
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	18

Mass center Coordinates

X	Y	Z
-6.54863	13.7648	-25.9354

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
C6P	CE1	PHE- 92	3.86	0	Hydrophobic	false
C1P	CG	GLN- 267	4.31	0	Hydrophobic	false
C1P	CG	GLU- 294	3.83	0	Hydrophobic	false
N6A	O	ILE- 364	2.82	134.81	H-Bond (Ligand Donor)	false
C1B	CD1	ILE- 364	4.49	0	Hydrophobic	false
CDP	CG1	ILE- 364	4.08	0	Hydrophobic	false
CEP	CD1	ILE- 364	4.1	0	Hydrophobic	false
C1B	CE	MET- 383	4.19	0	Hydrophobic	false
C4B	SD	MET- 383	4.05	0	Hydrophobic	false
CEP	CG	MET- 383	3.75	0	Hydrophobic	false
O9P	ND2	ASN- 384	2.88	168.3	H-Bond (Protein Donor)	false
C2P	CB	SER- 389	4.36	0	Hydrophobic	false
C1P	CD2	PHE- 392	3.93	0	Hydrophobic	false
O8A	NZ	LYS- 408	3.85	0	Ionic (Protein Cationic)	false
O5P	O	HOH- 737	2.57	179.98	H-Bond (Protein Donor)	false
N6A	O	HOH- 782	3.05	164.15	H-Bond (Ligand Donor)	false
O9P	O	HOH- 819	2.9	140.69	H-Bond (Protein Donor)	false
N4P	O	HOH- 876	2.86	149.21	H-Bond (Ligand Donor)	false
O5A	O	HOH- 895	3.09	179.96	H-Bond (Protein Donor)	false