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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:

4k13

1.600 Å

X-ray

2013-04-04

Activity from ChEMBL: What is pChEMBL ?
MinMeanMedianStandard DeviationMaxCount
pChEMBL:7.6008.1708.0500.43010.37084
List of CHEMBLId :

CHEMBL218490


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:13.757
Number of residues:30
Including
Standard Amino Acids: 29
Non Standard Amino Acids: 1
Water Molecules: 0
Cofactors:
Metals: ZN

Cavity properties

LigandabilityVolume (Å3)
0.473374.625

% Hydrophobic% Polar
46.8553.15
According to VolSite

Ligand :
4k13_1 Structure
HET Code: ETS
Formula: C10H17N2O4S3
Molecular weight: 325.448 g/mol
DrugBank ID: DB00869
Buried Surface Area:59.83 %
Polar Surface area: 155.91 Å2
Number of
H-Bond Acceptors: 4
H-Bond Donors: 2
Rings: 2
Aromatic rings: 1
Anionic atoms: 0
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 3

Mass center Coordinates

XYZ
16.91644.0514.8459


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
C19CZ2TRP- 54.360Hydrophobic
O16NE2GLN- 923.02151.06H-Bond
(Protein Donor)
S1CG2VAL- 1213.580Hydrophobic
C15CD2LEU- 1313.880Hydrophobic
S1CD2LEU- 1983.780Hydrophobic
C6CD1LEU- 1983.880Hydrophobic
O12NTHR- 1992.96153.23H-Bond
(Protein Donor)
N13OG1THR- 1992.73166.51H-Bond
(Ligand Donor)
N13ZN ZN- 3012.040Metal Acceptor