scPDB - 3e6c entry

Protein Data Bank Entry:

PDB ID : 3e6c

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2008-08-15

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Cyclic nucleotide-binding protein
ID:	B8FW11_DESHD
AC:	B8FW11
Organism:	Desulfitobacterium hafniense
Reign:	Bacteria
TaxID:	272564
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	48.414
Number of residues:	20
Including
Standard Amino Acids:	17
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.037	347.625

% Hydrophobic	% Polar
65.05	34.95
According to VolSite

Ligand :

HET Code:	3C4
Formula:	C8H6ClO3
Molecular weight:	185.584 g/mol
DrugBank ID:	-
Buried Surface Area:	65.21 %
Polar Surface area:	60.36 Å2

Number of
H-Bond Acceptors:	3
H-Bond Donors:	1
Rings:	1
Aromatic rings:	1
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	2

Mass center Coordinates

X	Y	Z
2.43375	47.0285	-7.54592

Binding mode :

What is Poseview ?

2D View
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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
CD2	CD2	LEU- 63	3.95	0	Hydrophobic	false
OH	OH	TYR- 76	2.56	151.37	H-Bond (Ligand Donor)	false
CE2	CG2	ILE- 84	4.1	0	Hydrophobic	false
OH	N	GLY- 85	2.96	163.66	H-Bond (Protein Donor)	false
O1	NZ	LYS- 86	2.7	155.87	H-Bond (Protein Donor)	false
O1	NZ	LYS- 86	2.7	0	Ionic (Protein Cationic)	false
CA	CG	LYS- 86	4.1	0	Hydrophobic	false
CD2	CD	LYS- 86	3.83	0	Hydrophobic	false
CZ	CG	LYS- 86	4.2	0	Hydrophobic	false
O2	OG1	THR- 90	2.71	162.15	H-Bond (Protein Donor)	false
O2	ND2	ASN- 92	2.97	152.38	H-Bond (Protein Donor)	false
CL	CE2	TYR- 130	3.54	0	Hydrophobic	false
OH	NZ	LYS- 133	2.68	159.76	H-Bond (Protein Donor)	false
CL	CD	LYS- 133	3.82	0	Hydrophobic	false