scPDB - 1vp6 entry

Protein Data Bank Entry:

PDB ID : 1vp6

Resolution :1.700 Å

Experimental Method : X-ray

Deposition Date : 2004-10-14

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:	17.538
Number of residues:	27
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.563	425.250

% Hydrophobic	% Polar
52.38	47.62
According to VolSite

Ligand :

HET Code:	CMP
Formula:	C10H11N5O6P
Molecular weight:	328.198 g/mol
DrugBank ID:	DB02527
Buried Surface Area:	73.88 %
Polar Surface area:	167.48 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	2
Rings:	4
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	1

Mass center Coordinates

X	Y	Z
21.5589	-37.9507	9.774

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	4.11	0	Hydrophobic	false
C1'	CG1	VAL- 282	3.83	0	Hydrophobic	false
C2'	CB	PHE- 296	4.2	0	Hydrophobic	false
O3'	N	GLY- 297	3.45	120.67	H-Bond (Protein Donor)	false
O2'	N	GLY- 297	2.65	151.32	H-Bond (Protein Donor)	false
O2'	OE2	GLU- 298	3.2	145.92	H-Bond (Ligand Donor)	false
O2'	OE1	GLU- 298	2.73	140.75	H-Bond (Ligand Donor)	false
O3'	N	MET- 299	3.38	139.33	H-Bond (Protein Donor)	false
C3'	SD	MET- 299	3.79	0	Hydrophobic	false
O2P	N	ALA- 300	2.79	141.81	H-Bond (Protein Donor)	false
O2P	NH1	ARG- 307	3.03	158.76	H-Bond (Protein Donor)	false
C5'	CB	ARG- 307	4.44	0	Hydrophobic	false
O1P	OG	SER- 308	2.82	158.12	H-Bond (Protein Donor)	false
O1P	N	SER- 308	2.73	165.08	H-Bond (Protein Donor)	false
C4'	CG2	VAL- 311	3.8	0	Hydrophobic	false
C2'	CD	ARG- 348	4.41	0	Hydrophobic	false