Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
Protein Data Bank Entry:

2w0d

2.000 Å

X-ray

2008-08-13

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Macrophage metalloelastase
ID:MMP12_HUMAN
AC:P39900
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:3.4.24.65


Chains:

Chain Name:Percentage of Residues
within binding site
A21 %
C79 %


Ligand binding site composition:

B-Factor:4.885
Number of residues:29
Including
Standard Amino Acids: 27
Non Standard Amino Acids: 2
Water Molecules: 0
Cofactors:
Metals: ZN

Cavity properties

LigandabilityVolume (Å3)
0.4952079.000

% Hydrophobic% Polar
47.0852.92
According to VolSite

Ligand :
2w0d_3 Structure
HET Code: CGS
Formula: C18H23N3O5S
Molecular weight: 393.457 g/mol
DrugBank ID: DB07556
Buried Surface Area:54.75 %
Polar Surface area: 117.21 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: 8

Mass center Coordinates

XYZ
-17.276733.2425-29.7349


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
CG2CG1ILE- 1803.890Hydrophobic
CE1CBLEU- 1814.220Hydrophobic
C17CD1LEU- 1814.160Hydrophobic
O33NLEU- 1812.84177.17H-Bond
(Protein Donor)
N35OALA- 1822.79140.06H-Bond
(Ligand Donor)
CG1CBHIS- 1834.490Hydrophobic
CD1CG2THR- 2153.820Hydrophobic
COMCBHIS- 2183.650Hydrophobic
C20CBHIS- 2183.90Hydrophobic
CCCBPRO- 2384.080Hydrophobic
COMCD2TYR- 2404.180Hydrophobic
CD2CBTYR- 2403.920Hydrophobic
O47ZN ZN- 12642.140Metal Acceptor
O48ZN ZN- 12642.230Metal Acceptor