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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:

1hzz

2.500 Å

X-ray

2001-01-27

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:NAD(P) transhydrogenase subunit alpha part 1
ID:PNTAA_RHORT
AC:Q2RSB2
Organism:Rhodospirillum rubrum
Reign:Bacteria
TaxID:269796
EC Number:1.6.1.2


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:65.535
Number of residues:46
Including
Standard Amino Acids: 45
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.5881927.125

% Hydrophobic% Polar
46.4153.59
According to VolSite

Ligand :
1hzz_1 Structure
HET Code: NAD
Formula: C21H26N7O14P2
Molecular weight: 662.417 g/mol
DrugBank ID: -
Buried Surface Area:55.3 %
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
-8.732666.8745924.0732


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
C5NCDARG- 1274.140Hydrophobic
N7NOILE- 1283.05142.89H-Bond
(Ligand Donor)
O1NNVAL- 1822.9168.4H-Bond
(Protein Donor)
C2DCG2VAL- 1824.40Hydrophobic
O3BOD2ASP- 2022.53163.74H-Bond
(Ligand Donor)
O3BOD1ASP- 2023.22121.56H-Bond
(Ligand Donor)
O2BOD1ASP- 2022.68162.31H-Bond
(Ligand Donor)
N3ANVAL- 2033.43144.73H-Bond
(Protein Donor)
N1ANE2GLN- 2473.05157.07H-Bond
(Protein Donor)
C1BCBALA- 2654.060Hydrophobic
O4BNLEU- 2663.44143.76H-Bond
(Protein Donor)
O3DOHOH- 4113.07163.63H-Bond
(Ligand Donor)