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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:

1gzu

2.900 Å

X-ray

2002-06-06

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1
ID:NMNA1_HUMAN
AC:Q9HAN9
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:2.7.7.1


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:53.849
Number of residues:26
Including
Standard Amino Acids: 26
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.0131127.250

% Hydrophobic% Polar
43.4156.59
According to VolSite

Ligand :
1gzu_1 Structure
HET Code: NMN
Formula: C11H14N2O8P
Molecular weight: 333.211 g/mol
DrugBank ID: DB03227
Buried Surface Area:60.61 %
Polar Surface area: 178.89 Å2
Number of
H-Bond Acceptors: 8
H-Bond Donors: 3
Rings: 2
Aromatic rings: 1
Anionic atoms: 2
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 5

Mass center Coordinates

XYZ
-15.563557.609541.2175


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
O3PNSER- 162.74153.35H-Bond
(Protein Donor)
O3POGSER- 162.54149.93H-Bond
(Protein Donor)
O2POGSER- 163.44127.45H-Bond
(Protein Donor)
O3PNZLYS- 573.12127.13H-Bond
(Protein Donor)
O2PNZLYS- 572.89155.43H-Bond
(Protein Donor)
O3PNZLYS- 573.120Ionic
(Protein Cationic)
O2PNZLYS- 572.890Ionic
(Protein Cationic)
O2RNE1TRP- 923.13146.86H-Bond
(Protein Donor)
C3CBTHR- 954.290Hydrophobic
O7NLEU- 963.5138.19H-Bond
(Protein Donor)
C5RCD2LEU- 1593.750Hydrophobic
C5CGLEU- 1684.070Hydrophobic
DuArDuArTRP- 1693.760Aromatic Face/Face