scPDB - 3gpc entry

Protein Data Bank Entry:

PDB ID : 3gpc

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2009-03-23

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Acyl-coenzyme A synthetase ACSM2A, mitochondrial
ID:	ACS2A_HUMAN
AC:	Q08AH3
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	6.2.1.2

Chains:

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

Ligand binding site composition:

B-Factor:	20.446
Number of residues:	32
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.073	2720.250

% Hydrophobic	% Polar
37.22	62.78
According to VolSite

Ligand :

HET Code:	COA
Formula:	C21H32N7O16P3S
Molecular weight:	763.502 g/mol
DrugBank ID:	DB01992
Buried Surface Area:	52.59 %
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
-0.728462	-49.2071	44.4166

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
CAP	CZ2	TRP- 265	4.17	0	Hydrophobic	false
C9P	CE2	TRP- 265	4.11	0	Hydrophobic	false
N7A	N	GLY- 338	3.11	134.03	H-Bond (Protein Donor)	false
N6A	OE2	GLU- 359	3.34	143.83	H-Bond (Ligand Donor)	false
N6A	O	SER- 360	2.63	134.89	H-Bond (Ligand Donor)	false
C2B	CE1	TYR- 361	4.08	0	Hydrophobic	false
C3B	CB	GLN- 363	4.33	0	Hydrophobic	false
C5B	CB	GLN- 363	3.71	0	Hydrophobic	false
O2A	OG1	THR- 364	3.12	175.89	H-Bond (Protein Donor)	false
O2A	N	THR- 364	3.01	145.6	H-Bond (Protein Donor)	false
O2B	OD2	ASP- 446	3.04	154.57	H-Bond (Ligand Donor)	false
O2B	OD1	ASP- 446	2.76	140.19	H-Bond (Ligand Donor)	false
C2B	CE1	PHE- 458	4.15	0	Hydrophobic	false
O7A	CZ	ARG- 461	2.9	0	Ionic (Protein Cationic)	false
C9P	CB	THR- 555	3.96	0	Hydrophobic	false
CDP	CG	LYS- 557	3.8	0	Hydrophobic	false