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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:

1ro6

2.000 Å

X-ray

2003-12-01

Activity from ChEMBL: What is pChEMBL ?
MinMeanMedianStandard DeviationMaxCount
pChEMBL:5.8306.4506.6600.3606.6604

List of CHEMBLId :

CHEMBL63


Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:cAMP-specific 3',5'-cyclic phosphodiesterase 4B
ID:PDE4B_HUMAN
AC:Q07343
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:3.1.4.53


Chains:

Chain Name:Percentage of Residues
within binding site
B100 %


Ligand binding site composition:

B-Factor:34.187
Number of residues:28
Including
Standard Amino Acids: 26
Non Standard Amino Acids: 2
Water Molecules: 0
Cofactors:
Metals: ZN MN

Cavity properties

LigandabilityVolume (Å3)
1.137843.750

% Hydrophobic% Polar
56.4043.60
According to VolSite

Ligand :
1ro6_2 Structure
HET Code: ROL
Formula: C16H21NO3
Molecular weight: 275.343 g/mol
DrugBank ID: DB04149
Buried Surface Area:65.98 %
Polar Surface area: 47.56 Å2
Number of
H-Bond Acceptors: 3
H-Bond Donors: 1
Rings: 3
Aromatic rings: 1
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 4

Mass center Coordinates

XYZ
19.9221111.01929.3028


Binding mode :
What is Poseview ?
  • 2D View
  • 3D View
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
C2CE2TYR- 2333.770Hydrophobic
O1NE2HIS- 2342.76146.12H-Bond
(Protein Donor)
N1OD2ASP- 3923.04123.84H-Bond
(Ligand Donor)
C3CD2LEU- 3934.470Hydrophobic
C16CBASN- 3954.480Hydrophobic
C16CE1TYR- 4034.020Hydrophobic
C16CBTHR- 4074.250Hydrophobic
C5CD1ILE- 4104.320Hydrophobic
C8CG2ILE- 4103.790Hydrophobic
C2CD1ILE- 4104.180Hydrophobic
C15CG1ILE- 4103.990Hydrophobic
C16CG2ILE- 4103.740Hydrophobic
C7CG1ILE- 4103.90Hydrophobic
C9CG1ILE- 4104.280Hydrophobic
C14SDMET- 4113.670Hydrophobic
C15CZPHE- 4143.710Hydrophobic
C13SDMET- 4313.830Hydrophobic
C13CBSER- 4423.360Hydrophobic
O3NE2GLN- 4433.42152.81H-Bond
(Protein Donor)
O2NE2GLN- 4433.02139.4H-Bond
(Protein Donor)
C11CGPHE- 4464.250Hydrophobic
C12CBPHE- 4463.590Hydrophobic