scPDB - 2wd9 entry

Protein Data Bank Entry:

PDB ID : 2wd9

Resolution :2.600 Å

Experimental Method : X-ray

Deposition Date : 2009-03-21

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:	15.593
Number of residues:	27
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.232	536.625

% Hydrophobic	% Polar
52.20	47.80
According to VolSite

Ligand :

HET Code:	IBP
Formula:	C13H17O2
Molecular weight:	205.273 g/mol
DrugBank ID:	DB09213
Buried Surface Area:	54.8 %
Polar Surface area:	40.12 Å2

Number of
H-Bond Acceptors:	2
H-Bond Donors:	0
Rings:	1
Aromatic rings:	1
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
27.7649	-34.3681	-3.78887

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
C4	CG2	ILE- 266	4.46	0	Hydrophobic	false
C10	CG2	ILE- 266	3.45	0	Hydrophobic	false
C4	CD1	LEU- 267	3.46	0	Hydrophobic	false
C4	CG1	VAL- 337	3.8	0	Hydrophobic	false
C12	CG2	VAL- 337	4.11	0	Hydrophobic	false
C5	CG2	VAL- 337	4.01	0	Hydrophobic	false
O2	N	THR- 364	3.25	163.08	H-Bond (Protein Donor)	false
O2	OG1	THR- 364	3.11	141.05	H-Bond (Protein Donor)	false
C5	CB	LEU- 368	4.43	0	Hydrophobic	false
O2	NH1	ARG- 472	3.12	167.58	H-Bond (Protein Donor)	false
C6	CB	ARG- 472	4.37	0	Hydrophobic	false