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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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PDB Description
Binding Site
Binding Site Similarity
Cavity Similarity
Ligand
Binding Mode
Binding Mode Similarity
Protein Data Bank Entry:

3d8w

1.700 Å

X-ray

2008-05-26

Activity from ChEMBL: What is pChEMBL ?
MinMeanMedianStandard DeviationMaxCount
pChEMBL:8.0508.0508.0500.0008.05035
List of CHEMBLId :

CHEMBL73962


Interactomes:
Interactome scPDB Proteins-Proteins
Interactome scPDB Proteins-Ligands
Interactome scPDB Ligands-Proteins
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Carbonic anhydrase 2
ID:CAH2_HUMAN
AC:P00918
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:4.2.1.1

Chains:

Chain Name:Percentage of Residues
within binding site
A100 %

Ligand binding site composition:

B-Factor:15.065
Number of residues:27
Including
Standard Amino Acids: 25
Non Standard Amino Acids: 1
Water Molecules: 1
Cofactors:
Metals: ZN

Cavity properties

LigandabilityVolume (Å3)
0.370357.750

% Hydrophobic% Polar
50.9449.06
According to VolSite

Ligand :
3d8w_1 Structure
HET Code: D8W
Formula: C8H8N4O4S3
Molecular weight: 320.369 g/mol
DrugBank ID: DB07050
Buried Surface Area:57.62 %
Polar Surface area: 177.11 Å2
Number of
H-Bond Acceptors: 6
H-Bond Donors: 2
Rings: 2
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 4

Mass center Coordinates

XYZ
-4.636164.5238914.5739


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
O2NE2GLN- 923.19164.94H-Bond
(Protein Donor)
S2CG2VAL- 1213.990Hydrophobic
C2CG1VAL- 1354.080Hydrophobic
S2CD2LEU- 1983.830Hydrophobic
C2CD1LEU- 1983.540Hydrophobic
O3NTHR- 1993.03151.9H-Bond
(Protein Donor)
N4OG1THR- 1992.87153.49H-Bond
(Ligand Donor)
N2OG1THR- 2003.22120.93H-Bond
(Protein Donor)
N3OG1THR- 2003.14152.83H-Bond
(Protein Donor)
C3CGPRO- 2024.430Hydrophobic
N4ZN ZN- 2621.950Metal Acceptor