scPDB - 1vpm entry

Protein Data Bank Entry:

PDB ID : 1vpm

Resolution :1.660 Å

Experimental Method : X-ray

Deposition Date : 2004-11-11

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Acyl-CoA hydrolase
ID:	Q9KEQ1_BACHD
AC:	Q9KEQ1
Organism:	Bacillus halodurans
Reign:	Bacteria
TaxID:	272558
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
B	42 %
C	58 %

Ligand binding site composition:

B-Factor:	29.092
Number of residues:	39
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.122	313.875

% Hydrophobic	% Polar
52.69	47.31
According to VolSite

Ligand :

HET Code:	COA
Formula:	C21H32N7O16P3S
Molecular weight:	763.502 g/mol
DrugBank ID:	DB01992
Buried Surface Area:	50.69 %
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
29.9974	79.3094	35.7662

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
S1P	CG2	ILE- 29	3.87	0	Hydrophobic	false
C2P	CG2	VAL- 34	4.05	0	Hydrophobic	false
CEP	CG2	VAL- 55	4.2	0	Hydrophobic	false
C6P	CG2	VAL- 55	3.82	0	Hydrophobic	false
N4P	O	THR- 56	2.87	154.11	H-Bond (Ligand Donor)	false
CDP	CB	ALA- 57	3.64	0	Hydrophobic	false
N1A	OG	SER- 58	2.79	169.5	H-Bond (Protein Donor)	false
N6A	OD1	ASP- 63	2.78	167.53	H-Bond (Ligand Donor)	false
N8P	O	PHE- 64	3.05	141.42	H-Bond (Ligand Donor)	false
C6P	CB	PHE- 64	4.03	0	Hydrophobic	false
S1P	CD1	PHE- 64	3.69	0	Hydrophobic	false
O8A	N	ARG- 85	2.78	138.97	H-Bond (Protein Donor)	false
O8A	N	THR- 86	3.31	148.09	H-Bond (Protein Donor)	false
O9A	N	THR- 86	3.04	144.64	H-Bond (Protein Donor)	false
O9A	OG1	THR- 86	2.57	173.24	H-Bond (Protein Donor)	false
C1B	CB	SER- 87	4.47	0	Hydrophobic	false
C4B	CB	SER- 87	4.33	0	Hydrophobic	false
O8A	N	SER- 87	3.42	131.53	H-Bond (Protein Donor)	false
O8A	OG	SER- 87	2.71	149.28	H-Bond (Protein Donor)	false
S1P	CG2	THR- 107	3.71	0	Hydrophobic	false
C1B	CG2	VAL- 115	4.34	0	Hydrophobic	false
C4B	CG2	VAL- 115	3.87	0	Hydrophobic	false
C5B	CG1	VAL- 115	4.26	0	Hydrophobic	false
CEP	CG1	VAL- 115	4.23	0	Hydrophobic	false
C5B	CG	PRO- 123	3.84	0	Hydrophobic	false
CEP	CG	PRO- 123	4.32	0	Hydrophobic	false