scPDB - 3ubm entry

Protein Data Bank Entry:

PDB ID : 3ubm

Resolution :1.990 Å

Experimental Method : X-ray

Deposition Date : 2011-10-24

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:	A9X6P7_ACEAC
AC:	A9X6P7
Organism:	Acetobacter aceti
Reign:	Bacteria
TaxID:	435
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	25.173
Number of residues:	41
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.431	722.250

% Hydrophobic	% Polar
43.46	56.54
According to VolSite

Ligand :

HET Code:	COA
Formula:	C21H32N7O16P3S
Molecular weight:	763.502 g/mol
DrugBank ID:	DB01992
Buried Surface Area:	63.46 %
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
-33.5741	-7.03398	129.386

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
CEP	CG2	VAL- 22	4.07	0	Hydrophobic	false
C2P	CB	VAL- 22	3.67	0	Hydrophobic	false
O5P	OG	SER- 24	3.06	140.88	H-Bond (Protein Donor)	false
O1A	CZ	ARG- 44	3.95	0	Ionic (Protein Cationic)	false
O1A	NH2	ARG- 44	3.19	160.85	H-Bond (Protein Donor)	false
N6A	O	LEU- 78	2.77	166.18	H-Bond (Ligand Donor)	false
N1A	N	THR- 80	3.17	153.03	H-Bond (Protein Donor)	false
O3B	NZ	LYS- 81	3.48	133.78	H-Bond (Protein Donor)	false
O7A	NZ	LYS- 81	3.9	0	Ionic (Protein Cationic)	false
O8A	NZ	LYS- 81	3.54	0	Ionic (Protein Cationic)	false
N8P	O	ASN- 102	2.64	145.25	H-Bond (Ligand Donor)	false
O5P	ND2	ASN- 102	3.45	140.35	H-Bond (Protein Donor)	false
C2B	CG	PHE- 103	4.43	0	Hydrophobic	false
O8A	NH2	ARG- 104	2.59	143.61	H-Bond (Protein Donor)	false
O9A	NH2	ARG- 104	2.96	122.42	H-Bond (Protein Donor)	false
O2A	N	ARG- 104	2.88	147.16	H-Bond (Protein Donor)	false
O8A	CZ	ARG- 104	3.63	0	Ionic (Protein Cationic)	false
O9A	CZ	ARG- 104	3.06	0	Ionic (Protein Cationic)	false
CAP	CB	ARG- 104	4.11	0	Hydrophobic	false
C3B	CB	ALA- 107	3.85	0	Hydrophobic	false
O7A	CZ	ARG- 110	3.41	0	Ionic (Protein Cationic)	false
O9A	CZ	ARG- 110	3.57	0	Ionic (Protein Cationic)	false
O7A	NH2	ARG- 110	3.43	123.97	H-Bond (Protein Donor)	false
O7A	NE	ARG- 110	2.56	170.36	H-Bond (Protein Donor)	false
O9A	NH2	ARG- 110	2.7	164.95	H-Bond (Protein Donor)	false
C2B	CE	MET- 111	4.16	0	Hydrophobic	false
C6P	CG2	VAL- 130	4	0	Hydrophobic	false
C6P	CB	ALA- 144	3.87	0	Hydrophobic	false
CDP	CE2	TYR- 145	4.12	0	Hydrophobic	false
C6P	SD	MET- 219	3.31	0	Hydrophobic	false
S1P	CE	MET- 219	3.25	0	Hydrophobic	false