Protein profile

PA4006

nicotinic acid mononucleotide adenylyltransferase

Genome: NC_002516.2

Gene: nadD PA4006 Structure source: Experimental + AlphaFold UniProt Q9HX21
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Amino acids 214
Annotations 8
Features 16
PDB binders 9
Druggability 0.833

Overview

Basic information about this protein and its source genome.

Accession
PA4006
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
nadD PA4006
Status
annotated
Amino acids
214
Structure source
Experimental + AlphaFold
EC
2.7.7.18
GO
GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. GO:0000309 Catalysis of the reaction: beta-nicotinamide D-ribonucleotide + ATP + H+ = diphosphate + NAD+. GO:0004515 Catalysis of the reaction: nicotinate beta-D-ribonucleotide + ATP + H+ = deamido-NAD+ + diphosphate. GO:0009435 The chemical reactions and pathways resulting in the formation of nicotinamide adenine dinucleotide (NAD+), a coenzyme that interconverts with its reduced form, NADH, in many redox and catabolic reactions. NAD+ is derived from various sources including vitamin B3. GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. GO:0016779 Catalysis of the transfer of a nucleotidyl group from one compound (donor) to another (acceptor).

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
58.824
Human E-value
4.3e-06
Gut microbiome off-target
hit
Essential (DEG)
Y
Localization
Cytoplasmic

Selected Druggability evidence

Selected Druggability is the FPocket score chosen for ranking using the curated structure priority. The 3D viewer may show a different loaded structure, so its visible pockets can differ.

FPocket 0.833
Structure –
Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

7
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0000309 Catalysis of the reaction: beta-nicotinamide D-ribonucleotide + ATP + H+ = diphosphate + NAD+.
  • GO:0004515 Catalysis of the reaction: nicotinate beta-D-ribonucleotide + ATP + H+ = deamido-NAD+ + diphosphate.
  • GO:0009435 The chemical reactions and pathways resulting in the formation of nicotinamide adenine dinucleotide (NAD+), a coenzyme that interconverts with its reduced form, NADH, in many redox and catabolic reactions. NAD+ is derived from various sources including vitamin B3.
  • GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
  • GO:0016779 Catalysis of the transfer of a nucleotidyl group from one compound (donor) to another (acceptor).
  • GO:0009058 A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.

Sequence Features

Domain/signature hits from InterPro and related databases.

16 records
Show feature table
Start End DB Term Name
3 211 Hamap MF_00244 Probable nicotinate-nucleotide adenylyltransferase [nadD].
3 211 InterPro IPR005248 Nicotinate/nicotinamide nucleotide adenylyltransferase
5 68 NCBIfam TIGR00125 cytidyltransferase-like domain
5 68 InterPro IPR004821 Cytidyltransferase-like domain
2 214 Gene3D G3DSA:3.40.50.620 HUPs
2 214 InterPro IPR014729 Rossmann-like alpha/beta/alpha sandwich fold
5 210 CDD cd02165 NMNAT
5 210 InterPro IPR005248 Nicotinate/nicotinamide nucleotide adenylyltransferase
7 184 Pfam PF01467 Cytidylyltransferase-like
7 184 InterPro IPR004821 Cytidyltransferase-like domain
2 214 FunFam G3DSA:3.40.50.620:FF:000291 Probable nicotinate-nucleotide adenylyltransferase
1 211 PANTHER PTHR39321 NICOTINATE-NUCLEOTIDE ADENYLYLTRANSFERASE-RELATED
1 211 InterPro IPR005248 Nicotinate/nicotinamide nucleotide adenylyltransferase
7 210 NCBIfam TIGR00482 nicotinate (nicotinamide) nucleotide adenylyltransferase
7 210 InterPro IPR005248 Nicotinate/nicotinamide nucleotide adenylyltransferase
1 211 SUPERFAMILY SSF52374 Nucleotidylyl transferase

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

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Structural evidence

3 + 1

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
PDB 1YUM
X-ray 1.70 Å A,B,C,D
100.0% 1-214
PDBe RCSB PDBj File
Viewing
PDB 1YUL
X-ray 2.00 Å A
100.0% 1-214
PDBe RCSB PDBj File
Loaded
PDB 1YUN
X-ray 2.00 Å A,B
100.0% 1-214
PDBe RCSB PDBj File
Loaded
AlphaFold PA4006
AlphaFold — — full sequence — Loaded
Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

Pockets (FPOCKET)

Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).

FPOCKET Sticks Spheres Surfaces Druggability Labels Zoom Positions
1 0.833
2 0.707
3 0.335

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK Sticks Spheres Surfaces Score Probability Labels Zoom Positions
1 24.3 0.897

Ligand evidence

Ligands grouped by evidence source. PDB ligands keep the source crystal visible, and loaded crystals can be opened directly in the structure viewer.

59 records

Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in TPW, use Open crystal to inspect it in the structure viewer.

Show only:
Ligand Source crystal MW · LogP · TPSA Lipinski PAINS SMILES
NCN
1YUM 1.70 Å Open crystal
335.2 Da LogP -2.23 TPSA 160.5 ✓ Ro5 ✓ Clean c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P…

PDB and ChEMBL records on this protein are shown in full. ChEMBL records from similar proteins are capped at the top 100 per protein (by pchembl) and ZINC at the top 50 (Tanimoto ≥ 0.5). ADME columns are descriptor-based screening flags, not experimental toxicity results.