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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:

3kmc

1.800 Å

X-ray

2009-11-10

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
B100 %


Ligand binding site composition:

B-Factor:27.751
Number of residues:28
Including
Standard Amino Acids: 26
Non Standard Amino Acids: 1
Water Molecules: 1
Cofactors:
Metals: ZN

Cavity properties

LigandabilityVolume (Å3)
0.060361.125

% Hydrophobic% Polar
38.3261.68
According to VolSite

Ligand :
3kmc_2 Structure
HET Code: 403
Formula: C20H24ClN3O4S
Molecular weight: 437.940 g/mol
DrugBank ID: -
Buried Surface Area:58.16 %
Polar Surface area: 121.35 Å2
Number of
H-Bond Acceptors: 5
H-Bond Donors: 3
Rings: 3
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 7

Mass center Coordinates

XYZ
50.177233.372640.5691


Binding mode :
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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
O10ZN ZN- 22.450Metal Acceptor
O21ZN ZN- 22.080Metal Acceptor
O22ZN ZN- 22.340Metal Acceptor
O17NLEU- 3483.16163.68H-Bond
(Protein Donor)
C23CBLEU- 3483.950Hydrophobic
O17NGLY- 3493.3148.76H-Bond
(Protein Donor)
C23CG2VAL- 4024.060Hydrophobic
DuArDuArHIS- 4053.970Aromatic Face/Face
O21OE1GLU- 4063.01129.2H-Bond
(Ligand Donor)
O21OE2GLU- 4062.72165.99H-Bond
(Ligand Donor)
S8CBALA- 4394.050Hydrophobic
C23CBALA- 4393.90Hydrophobic