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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:

4nmj

2.000 Å

X-ray

2013-11-15

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Aldehyde dehydrogenase
ID:G7VCG0_9CREN
AC:G7VCG0
Organism:Pyrobaculum ferrireducens
Reign:Archaea
TaxID:1104324
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
D100 %


Ligand binding site composition:

B-Factor:21.031
Number of residues:35
Including
Standard Amino Acids: 33
Non Standard Amino Acids: 0
Water Molecules: 2
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.874978.750

% Hydrophobic% Polar
43.1056.90
According to VolSite

Ligand :
4nmj_1 Structure
HET Code: NAP
Formula: C21H25N7O17P3
Molecular weight: 740.381 g/mol
DrugBank ID: DB03461
Buried Surface Area:71.66 %
Polar Surface area: 405.54 Å2
Number of
H-Bond Acceptors: 21
H-Bond Donors: 5
Rings: 5
Aromatic rings: 3
Anionic atoms: 4
Cationic atoms: 1
Rule of Five Violation: 2
Rotatable Bonds: 13

Mass center Coordinates

XYZ
41.994854.822174.2173


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- 1513.660Hydrophobic
C4BCG2ILE- 1513.540Hydrophobic
O3BOTHR- 1522.8161.38H-Bond
(Ligand Donor)
O1NNE1TRP- 1543.03139.24H-Bond
(Protein Donor)
O2BNZLYS- 1782.75143.64H-Bond
(Protein Donor)
C3BCBALA- 1804.420Hydrophobic
C1BCE1PHE- 2294.290Hydrophobic
C4BCE1PHE- 2293.620Hydrophobic
O1ANGLU- 2322.94164.7H-Bond
(Protein Donor)
O3NGLU- 2323.29130.47H-Bond
(Protein Donor)
O1AOG1THR- 2352.64156.41H-Bond
(Protein Donor)