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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:

3iwk

2.400 Å

X-ray

2009-09-02

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Aminoaldehyde dehydrogenase
ID:Q8VWZ1_PEA
AC:Q8VWZ1
Organism:Pisum sativum
Reign:Eukaryota
TaxID:3888
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
F100 %


Ligand binding site composition:

B-Factor:27.921
Number of residues:41
Including
Standard Amino Acids: 40
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.962891.000

% Hydrophobic% Polar
41.6758.33
According to VolSite

Ligand :
3iwk_6 Structure
HET Code: NAD
Formula: C21H26N7O14P2
Molecular weight: 662.417 g/mol
DrugBank ID: -
Buried Surface Area:48.78 %
Polar Surface area: 343.54 Å2
Number of
H-Bond Acceptors: 18
H-Bond Donors: 6
Rings: 5
Aromatic rings: 3
Anionic atoms: 2
Cationic atoms: 1
Rule of Five Violation: 3
Rotatable Bonds: 11

Mass center Coordinates

XYZ
16.934914.498814.2645


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
C5NCBPRO- 1603.370Hydrophobic
C2DCZ2TRP- 1614.180Hydrophobic
C4BCBHIS- 2194.390Hydrophobic
C1BCBHIS- 2194.210Hydrophobic
N6AOGLY- 2223.37122.37H-Bond
(Ligand Donor)
C4DCBSER- 2394.440Hydrophobic
O1NOG1THR- 2423.35149.52H-Bond
(Protein Donor)
O3BNZLYS- 2453.29120.58H-Bond
(Protein Donor)
O2BNZLYS- 2452.73167.91H-Bond
(Protein Donor)
C2BCDLYS- 2454.470Hydrophobic
C4NSGCYS- 2944.260Hydrophobic