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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Protein Data Bank Entry:

4kl1

2.700 Å

X-ray

2013-05-07

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4
ID:HCN4_HUMAN
AC:Q9Y3Q4
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A85 %
C15 %


Ligand binding site composition:

B-Factor:42.332
Number of residues:20
Including
Standard Amino Acids: 19
Non Standard Amino Acids: 1
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.7991144.125

% Hydrophobic% Polar
35.9964.01
According to VolSite

Ligand :
4kl1_2 Structure
HET Code: PCG
Formula: C10H11N5O7P
Molecular weight: 344.197 g/mol
DrugBank ID: -
Buried Surface Area:50.57 %
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

XYZ
33.2313-15.524-21.8859


Binding mode :
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Binding mode
BioSolveIT 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
BioSolveIT


LigandProteinInteraction
AtomAtomResidueDistance
(Å)
Angle (°)Type
C3'CE2PHE- 5404.420Hydrophobic
O2'NE2HIS- 5413.26162.33H-Bond
(Protein Donor)
N2OTYR- 5592.96132.36H-Bond
(Ligand Donor)
N1OLYS- 5622.6162.4H-Bond
(Ligand Donor)
N2OLYS- 5623.08131.88H-Bond
(Ligand Donor)
O6NPHE- 5642.88133.99H-Bond
(Protein Donor)
O2'OE1GLU- 5662.79171.92H-Bond
(Ligand Donor)
O2'OE2GLU- 5663.33120.63H-Bond
(Ligand Donor)
C5'CE2PHE- 6133.580Hydrophobic
C4'CD2PHE- 6134.320Hydrophobic