scPDB - 3cl1 entry

Protein Data Bank Entry:

PDB ID : 3cl1

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 2008-03-18

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Cyclic nucleotide-gated potassium channel mll3241
ID:	CNGK1_RHILO
AC:	Q98GN8
Organism:	Rhizobium loti
Reign:	Bacteria
TaxID:	266835
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	15.242
Number of residues:	27
Including
Standard Amino Acids:	26
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	CL

Cavity properties

Ligandability	Volume (Å3)
0.816	297.000

% Hydrophobic	% Polar
57.95	42.05
According to VolSite

Ligand :

HET Code:	PCG
Formula:	C10H11N5O7P
Molecular weight:	344.197 g/mol
DrugBank ID:	-
Buried Surface Area:	75.72 %
Polar Surface area:	183.16 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	3
Rings:	4
Aromatic rings:	1
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	1

Mass center Coordinates

X	Y	Z
-2.91883	90.2007	8.04396

Binding mode :

What is Poseview ?

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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
C5'	SG	CYS- 263	4.32	0	Hydrophobic	false
C1'	CG2	VAL- 282	4.22	0	Hydrophobic	false
C1'	CB	PHE- 296	3.85	0	Hydrophobic	false
O3'	N	GLY- 297	3.44	122.09	H-Bond (Protein Donor)	false
O2'	N	GLY- 297	2.62	151.71	H-Bond (Protein Donor)	false
O2'	OE1	GLU- 298	2.79	122.6	H-Bond (Ligand Donor)	false
O2'	OE2	GLU- 298	2.78	163.84	H-Bond (Ligand Donor)	false
C3'	SD	MET- 299	3.77	0	Hydrophobic	false
O2A	N	ALA- 300	2.98	148.55	H-Bond (Protein Donor)	false
O2A	NH1	ARG- 307	2.9	161.35	H-Bond (Protein Donor)	false
O1A	N	SER- 308	2.92	164.01	H-Bond (Protein Donor)	false
O1A	OG	SER- 308	2.75	149.63	H-Bond (Protein Donor)	false
N2	OG	SER- 308	2.66	174.27	H-Bond (Ligand Donor)	false
C5'	CB	ALA- 309	4.23	0	Hydrophobic	false
C5'	CG2	VAL- 311	3.92	0	Hydrophobic	false
O2'	NH1	ARG- 348	3.4	120.88	H-Bond (Protein Donor)	false
C2'	CD	ARG- 348	4.07	0	Hydrophobic	false