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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:

4j16

2.410 Å

X-ray

2013-02-01

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:NAD/NADP transhydrogenase alpha subunit 1
ID:Q72GR8_THET2
AC:Q72GR8
Organism:Thermus thermophilus
Reign:Bacteria
TaxID:262724
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:65.832
Number of residues:33
Including
Standard Amino Acids: 30
Non Standard Amino Acids: 0
Water Molecules: 3
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.3111373.625

% Hydrophobic% Polar
46.6853.32
According to VolSite

Ligand :
4j16_1 Structure
HET Code: NAD
Formula: C21H26N7O14P2
Molecular weight: 662.417 g/mol
DrugBank ID: -
Buried Surface Area:37.71 %
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
28.250614.3221-13.4744


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
C3BCG2VAL- 1983.990Hydrophobic
C2BCG1VAL- 1983.710Hydrophobic
O1ANH1ARG- 1992.86146.78H-Bond
(Protein Donor)
O1ANEARG- 1992.91147.86H-Bond
(Protein Donor)
O1ACZARG- 1993.320Ionic
(Protein Cationic)
C5BCBALA- 2563.760Hydrophobic
C3DCBGLN- 2573.940Hydrophobic
C4BCGPRO- 2643.990Hydrophobic
C2BCD2LEU- 2664.270Hydrophobic