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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:

3dd8

1.900 Å

X-ray

2008-06-05

Activity from ChEMBL: What is pChEMBL ?
MinMeanMedianStandard DeviationMaxCount
pChEMBL:7.8507.8507.8500.0007.8501
List of CHEMBLId :

CHEMBL476937


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:4.020
Number of residues:27
Including
Standard Amino Acids: 26
Non Standard Amino Acids: 1
Water Molecules: 0
Cofactors:
Metals: ZN

Cavity properties

LigandabilityVolume (Å3)
0.273347.625

% Hydrophobic% Polar
44.6655.34
According to VolSite

Ligand :
3dd8_1 Structure
HET Code: 2C7
Formula: C16H21NO5S2
Molecular weight: 371.472 g/mol
DrugBank ID: DB06954
Buried Surface Area:51.68 %
Polar Surface area: 120.29 Å2
Number of
H-Bond Acceptors: 5
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
-3.088215.4169614.348


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
CALCG1VAL- 1214.320Hydrophobic
CAMCG2VAL- 1213.850Hydrophobic
CAGCE1PHE- 1314.330Hydrophobic
CADCG2VAL- 1353.810Hydrophobic
CAGCD1LEU- 1984.160Hydrophobic
CASCD2LEU- 1983.920Hydrophobic
OAANTHR- 1992.87155.56H-Bond
(Protein Donor)
NAVOG1THR- 1992.78144.25H-Bond
(Ligand Donor)
CARCG2THR- 2004.480Hydrophobic
CACCGPRO- 2023.740Hydrophobic
CADCD1LEU- 2043.760Hydrophobic
NAVZN ZN- 2621.930Metal Acceptor