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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:

4i3w

2.240 Å

X-ray

2012-11-26

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Aldehyde dehydrogenase (NAD+)
ID:Q92UV7_RHIME
AC:Q92UV7
Organism:Rhizobium meliloti
Reign:Bacteria
TaxID:266834
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
C97 %
G3 %


Ligand binding site composition:

B-Factor:22.080
Number of residues:37
Including
Standard Amino Acids: 34
Non Standard Amino Acids: 0
Water Molecules: 3
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.5301127.250

% Hydrophobic% Polar
49.4050.60
According to VolSite

Ligand :
4i3w_3 Structure
HET Code: NAD
Formula: C21H26N7O14P2
Molecular weight: 662.417 g/mol
DrugBank ID: -
Buried Surface Area:52.8 %
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
69.9409-72.134916.4447


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
C1BCG2ILE- 1543.850Hydrophobic
C4BCG2ILE- 1543.690Hydrophobic
O3BOTHR- 1552.74152.88H-Bond
(Ligand Donor)
C5BCBPRO- 1564.160Hydrophobic
O2NNPHE- 1573.22147.01H-Bond
(Protein Donor)
C3DCE2PHE- 1573.790Hydrophobic
O3BNZLYS- 1812.9159.6H-Bond
(Protein Donor)
O2BNZLYS- 1813.27122.28H-Bond
(Protein Donor)
C3BCBTHR- 1833.610Hydrophobic
O2BOE1GLU- 1843.06127.4H-Bond
(Ligand Donor)
C3DCD1LEU- 1853.840Hydrophobic
C4BCE1PHE- 2323.830Hydrophobic
O1ANSER- 2352.98167.23H-Bond
(Protein Donor)
O1AOGSER- 2352.95153.58H-Bond
(Protein Donor)
O3NSER- 2353.43121.48H-Bond
(Protein Donor)
C1DCG2ILE- 3344.430Hydrophobic
O2DNE2HIS- 3353.28168.54H-Bond
(Protein Donor)