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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:

3dz4

1.840 Å

X-ray

2008-07-29

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:S-adenosylmethionine decarboxylase proenzyme
ID:DCAM_HUMAN
AC:P17707
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:4.1.1.50


Chains:

Chain Name:Percentage of Residues
within binding site
B36 %
A64 %


Ligand binding site composition:

B-Factor:21.793
Number of residues:27
Including
Standard Amino Acids: 27
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.675398.250

% Hydrophobic% Polar
47.4652.54
According to VolSite

Ligand :
3dz4_1 Structure
HET Code: C8M
Formula: C15H24N7O4
Molecular weight: 366.396 g/mol
DrugBank ID: -
Buried Surface Area:69.64 %
Polar Surface area: 166.84 Å2
Number of
H-Bond Acceptors: 8
H-Bond Donors: 5
Rings: 3
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 1
Rule of Five Violation: 1
Rotatable Bonds: 6

Mass center Coordinates

XYZ
-27.1364-3.9294638.8543


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
C2'CGPHE- 73.990Hydrophobic
C3'CD2PHE- 74.050Hydrophobic
N1OLEU- 653.01152.32H-Bond
(Ligand Donor)
N3NGLU- 673.08164.6H-Bond
(Protein Donor)
N7OGLU- 673.32157.49H-Bond
(Ligand Donor)
C4SGCYS- 823.380Hydrophobic
C1'CBPHE- 2234.020Hydrophobic
C8CBPHE- 2233.990Hydrophobic
N1OGSER- 2292.92159.18H-Bond
(Ligand Donor)
C4CBHIS- 2434.180Hydrophobic
C3'CG2THR- 2453.950Hydrophobic
O2'OE2GLU- 2472.99146.8H-Bond
(Ligand Donor)
O3'OE1GLU- 2472.83136.58H-Bond
(Ligand Donor)