scPDB - 1vgr entry

Protein Data Bank Entry:

PDB ID : 1vgr

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2004-04-28

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Formyl-CoA:oxalate CoA-transferase
ID:	FCTA_OXAFO
AC:	O06644
Organism:	Oxalobacter formigenes
Reign:	Bacteria
TaxID:	847
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	91 %
B	9 %

Ligand binding site composition:

B-Factor:	51.572
Number of residues:	45
Including
Standard Amino Acids:	44
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.140	381.375

% Hydrophobic	% Polar
45.13	54.87
According to VolSite

Ligand :

HET Code:	COA
Formula:	C21H32N7O16P3S
Molecular weight:	763.502 g/mol
DrugBank ID:	DB01992
Buried Surface Area:	65.05 %
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
-39.4565	12.5887	26.3542

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
CDP	CG2	VAL- 16	4.41	0	Hydrophobic	false
C2P	CG1	VAL- 16	3.78	0	Hydrophobic	false
S1P	CB	VAL- 16	3.41	0	Hydrophobic	false
S1P	CB	GLN- 17	4.09	0	Hydrophobic	false
S1P	CB	ALA- 18	4.07	0	Hydrophobic	false
O4B	NH2	ARG- 38	3.12	130.53	H-Bond (Protein Donor)	false
N6A	O	LEU- 72	3.37	152.86	H-Bond (Ligand Donor)	false
C6P	CB	ASN- 96	4.09	0	Hydrophobic	false
C2B	CG	PHE- 97	4.41	0	Hydrophobic	false
C2B	CB	ALA- 101	4.16	0	Hydrophobic	false
O7A	CZ	ARG- 104	3.77	0	Ionic (Protein Cationic)	false
C1B	CE	MET- 105	4.23	0	Hydrophobic	false
C6P	CG1	VAL- 124	3.98	0	Hydrophobic	false
O2A	NZ	LYS- 137	3.09	0	Ionic (Protein Cationic)	false
O4A	NZ	LYS- 137	2.79	0	Ionic (Protein Cationic)	false
O4A	NZ	LYS- 137	2.79	162.36	H-Bond (Protein Donor)	false
CEP	CG	LYS- 137	3.63	0	Hydrophobic	false
O9P	N	VAL- 138	3.39	164.19	H-Bond (Protein Donor)	false
CDP	CE1	TYR- 139	3.99	0	Hydrophobic	false
CEP	CE2	TYR- 139	3.78	0	Hydrophobic	false
CCP	CZ	TYR- 139	4.2	0	Hydrophobic	false
C6P	SD	MET- 200	4.15	0	Hydrophobic	false