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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:

2i47

1.900 Å

X-ray

2006-08-21

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Disintegrin and metalloproteinase domain-containing protein 17
ID:ADA17_HUMAN
AC:P78536
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:3.4.24.86


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:12.724
Number of residues:28
Including
Standard Amino Acids: 25
Non Standard Amino Acids: 1
Water Molecules: 2
Cofactors:
Metals: ZN

Cavity properties

LigandabilityVolume (Å3)
0.320448.875

% Hydrophobic% Polar
39.8560.15
According to VolSite

Created with Highcharts 4.0.1Chart context menuDistribution of cavity propertiesscPDB Median2i47HydrophobicAromaticHBond AcceptorHBond DonorHBondAcceptor/DonorPositive IonizableNegativeIonizableDummy802040Highcharts.com
Ligand :
2i47_1 Structure
HET Code: INN
Formula: C19H38N5O5
Molecular weight: 416.536 g/mol
DrugBank ID: -
Buried Surface Area:51.39 %
Polar Surface area: 164.27 Å2
Number of
H-Bond Acceptors: 5
H-Bond Donors: 6
Rings: 0
Aromatic rings: 0
Anionic atoms: 0
Cationic atoms: 1
Rule of Five Violation: 1
Rotatable Bonds: 12

Mass center Coordinates

XYZ
-3.3457239.584349.7018
Created with Highcharts 4.0.1Chart context menuDistribution of ligand propertiesscPDB Median2i47RingsAromatic RingsHBond AcceptorHBond DonorRotatable BondsPositive IonizableNegativeIonizableRO5 Violation8051015Highcharts.com


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
N2OGLY- 3462.92160.36H-Bond
(Ligand Donor)
O1NLEU- 3482.81159.15H-Bond
(Protein Donor)
C12CD1LEU- 3484.340Hydrophobic
C3CD1LEU- 3484.020Hydrophobic
NOGLY- 3493.1165.45H-Bond
(Ligand Donor)
O3OHTYR- 3902.7171.86H-Bond
(Protein Donor)
C12CE1TYR- 3904.220Hydrophobic
C3CG2VAL- 4024.010Hydrophobic
C3CBHIS- 4054.120Hydrophobic
O4OE1GLU- 4062.73157.23H-Bond
(Protein Donor)
N1OPRO- 4373.3168.38H-Bond
(Ligand Donor)
O2NALA- 4392.89163.13H-Bond
(Protein Donor)
C12CBALA- 4394.30Hydrophobic
C2CBALA- 4393.90Hydrophobic
OZN ZN- 8022.140Metal Acceptor
O4ZN ZN- 8022.080Metal Acceptor
O4OHOH- 9582.65147.49H-Bond
(Protein Donor)