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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:

3i7g

1.950 Å

X-ray

2009-07-08

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Collagenase 3
ID:MMP13_HUMAN
AC:P45452
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:3.4.24


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:21.087
Number of residues:26
Including
Standard Amino Acids: 25
Non Standard Amino Acids: 1
Water Molecules: 0
Cofactors:
Metals: ZN

Cavity properties

LigandabilityVolume (Å3)
0.899405.000

% Hydrophobic% Polar
46.6753.33
According to VolSite

Ligand :
3i7g_1 Structure
HET Code: 732
Formula: C20H23ClN2O3
Molecular weight: 374.861 g/mol
DrugBank ID: -
Buried Surface Area:55.5 %
Polar Surface area: 71.34 Å2
Number of
H-Bond Acceptors: 2
H-Bond Donors: 2
Rings: 3
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 5

Mass center Coordinates

XYZ
-6.5935429.591354.6807


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
N20OGLY- 1833.14166.6H-Bond
(Ligand Donor)
C26CD2LEU- 1844.490Hydrophobic
O14NLEU- 1853.08165.63H-Bond
(Protein Donor)
C1CG2VAL- 2194.240Hydrophobic
DuArDuArHIS- 2223.970Aromatic Face/Face
C1CBHIS- 2223.630Hydrophobic
CL8CD1LEU- 2394.120Hydrophobic
C23CG1ILE- 2434.260Hydrophobic
O19NTYR- 2443.25172.49H-Bond
(Protein Donor)
C2CBTYR- 2444.410Hydrophobic