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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:

1b3d

2.300 Å

X-ray

1998-12-09

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Stromelysin-1
ID:MMP3_HUMAN
AC:P08254
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:3.4.24.17


Chains:

Chain Name:Percentage of Residues
within binding site
B100 %


Ligand binding site composition:

B-Factor:11.665
Number of residues:24
Including
Standard Amino Acids: 23
Non Standard Amino Acids: 1
Water Molecules: 0
Cofactors:
Metals: ZN

Cavity properties

LigandabilityVolume (Å3)
0.907543.375

% Hydrophobic% Polar
42.8657.14
According to VolSite

Ligand :
1b3d_1 Structure
HET Code: S27
Formula: C20H27N2O3P
Molecular weight: 374.414 g/mol
DrugBank ID: DB08507
Buried Surface Area:49.78 %
Polar Surface area: 79.45 Å2
Number of
H-Bond Acceptors: 3
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
-21.856828.6731-0.317462


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
C18CG1VAL- 1634.30Hydrophobic
C10CG1VAL- 1633.820Hydrophobic
C13CG2VAL- 1633.650Hydrophobic
C6CD1LEU- 1644.20Hydrophobic
C9CGLEU- 1643.570Hydrophobic
O8NLEU- 1642.74144.7H-Bond
(Protein Donor)
O8NALA- 1653.19152.12H-Bond
(Protein Donor)
NAOALA- 1653.07152.17H-Bond
(Ligand Donor)
C10CBHIS- 1663.720Hydrophobic
C5CG1VAL- 1983.670Hydrophobic
DuArDuArHIS- 2013.980Aromatic Face/Face
C4CBHIS- 2013.850Hydrophobic
C4CBTYR- 2233.90Hydrophobic
OAZN ZN- 3011.880Metal Acceptor
OBZN ZN- 3012.010Metal Acceptor