scPDB - 5frd entry

Protein Data Bank Entry:

PDB ID : 5frd

Resolution :1.400 Å

Experimental Method : X-ray

Deposition Date : 2015-12-17

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Carboxylesterase (Est-2)
ID:	O28735_ARCFU
AC:	O28735
Organism:	Archaeoglobus fulgidus
Reign:	Archaea
TaxID:	224325
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	17.238
Number of residues:	32
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	CL

Cavity properties

Ligandability	Volume (Å3)
0.962	300.375

% Hydrophobic	% Polar
51.69	48.31
According to VolSite

Ligand :

HET Code:	COA
Formula:	C21H32N7O16P3S
Molecular weight:	763.502 g/mol
DrugBank ID:	DB01992
Buried Surface Area:	48.02 %
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
-27.7536	14.3534	27.1975

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
N6A	O	ARG- 117	2.95	157.76	H-Bond (Ligand Donor)	false
O2A	CZ	ARG- 117	3.92	0	Ionic (Protein Cationic)	false
O2A	NH1	ARG- 117	2.91	157.7	H-Bond (Protein Donor)	false
C2P	CD2	LEU- 118	4.16	0	Hydrophobic	false
S1P	CB	LEU- 118	3.98	0	Hydrophobic	false
CCP	CB	ARG- 119	4.37	0	Hydrophobic	false
CDP	CB	ARG- 119	4.12	0	Hydrophobic	false
S1P	CG2	VAL- 120	4.02	0	Hydrophobic	false
CEP	CD1	LEU- 121	4.19	0	Hydrophobic	false
O5P	N	LEU- 121	2.82	172.55	H-Bond (Protein Donor)	false
C6P	CE	MET- 142	3.98	0	Hydrophobic	false
S1P	CD2	LEU- 169	4.4	0	Hydrophobic	false
S1P	CB	CYS- 172	3.81	0	Hydrophobic	false
C1B	CD2	LEU- 178	4.23	0	Hydrophobic	false
C6P	CD2	LEU- 202	4.31	0	Hydrophobic	false
N4P	O	LEU- 202	2.87	150.89	H-Bond (Ligand Donor)	false
C2P	CG2	THR- 203	4.49	0	Hydrophobic	false