KpKP13 Protein target profile

Nicotinate-nucleotide pyrophosphorylase carboxylating

Accession: KP13_01888

Gene: nadC AHE46328.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GJC5
Length 284
Pocket druggability (P2Rank · AlphaFold DB model) 0.583
Direct ligand evidence 0 54 total records
Functional annotation 1 EC 5 GO
Target summary

Target candidate with partial support; inspect missing evidence before prioritizing.

Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.

Terms and data sources used on this page

PDB: experimentally determined structures from the Protein Data Bank. These are the strongest structural evidence, but may cover only part of the protein.

AlphaFold DB model: a precomputed predicted structure downloaded from AlphaFold Database/UniProt, not an experiment performed here.

ColabFold model: a predicted structure generated for this workspace; interpret it with coverage and confidence.

pLDDT: confidence score for predicted structures. High values support local geometry; low values mean the region should not drive pocket interpretation.

FPocket / P2Rank: software tools that predict possible ligand-binding pockets on a 3D structure. They are useful screening signals, not experimental validation.

Druggability: a pocket-based estimate of whether a small molecule could bind productively. It does not mean a drug already exists.

PDB ligand: a compound observed in an experimental structure. Direct same-protein records are stronger than homolog-transferred records.

ChEMBL: a public database of measured compound bioactivity. Direct entries are stronger than entries transferred from similar proteins.

ZINC: a purchasable-compound database. Here it marks proposed candidates from chemical similarity, not measured binders.

LigQ / LigQ_2: an internal Target pipeline step that gathers PDB, ChEMBL, and ZINC ligand evidence for each protein.

Off-target: sequence similarity to proteins we prefer not to hit, such as human proteins or beneficial gut microbiome proteins.

DEG: Database of Essential Genes. A match suggests the protein resembles genes known to be essential in other organisms.

Roary / CoreCruncher: pan-genome tools used to decide whether a gene is core across analyzed strains or accessory/strain-specific.

EC / GO: functional annotations: EC describes enzyme reactions; GO describes biological process, molecular function, or cellular component.

KEGG pathway: a curated metabolic route label used here to group reactions imported from the metabolic model.

Chokepoint: a metabolic reaction that is the only producer or consumer of a metabolite in the imported model.

Prioritization evidence

Selectivity, essentiality, structural confidence, conservation, and predicted binding-site evidence.

Off-target risk

Human off-target
Hit
Human identity (%)
38.636 Lower values reduce human off-target concern.
Human E-value
1.06e-13
Gut microbiome similarity
3.5% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
56.727 Higher values support similarity to known essential genes.
DEG E-value
1.6e-101 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
97.41 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

P2Rank's binding-site probability is the primary druggability signal shown across the app; FPocket's druggability score is shown alongside it for comparison. Both estimate small-molecule pocket quality after applying the curated structure priority — neither is experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

Druggability (P2Rank) 0.583
Structure A0A0H3GJC5
Pocket Pocket 1
Druggability (FPocket) 0.283
Structure A0A0H3GJC5
Pocket Pocket 3
ColabFold model
P2Rank 0.586 · Pocket 1
FPocket 0.412 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 164 / 4744 genomes with a hit
Prevalence 3.5%

Sequence

Primary amino-acid sequence viewer.

MLLERINLDITDAVAHSLREDLGGEVDANNDISAQLLPQDARSHAVVITREDGVFCGKRWVEEVFIQLAGDDVNITWHVADGDAVKADQPLFELEGPSRILLTGERTALNFVQTLSGVASVVRRYVDLLAGTKTQLLDTRKTLPGLRTALKYAVLCGGGANHRLGLFDAFLIKENHIIASGSIRQAVEKAFWLHPDVPVEVEVETLDELEQALKAGADIIMLDNFTTDLMREAVKITAGQAALEVSGNVTFDTIREFADTGVDYISVGALTKHVQALDLSMRFR

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Subcellular localization

Localization
Cytoplasmic

Enzyme Commission (EC)

1

Gene Ontology (GO)

5
  • GO:0004514 Catalysis of the reaction: CO2 + diphosphate + nicotinate D-ribonucleotide = 5-phospho-alpha-D-ribose 1-diphosphate + 2 H+ + quinolinate.
  • 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:0016763 Catalysis of the transfer of a pentosyl group from one compound (donor) to another (acceptor).
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0034213 The chemical reactions and pathways resulting in the breakdown of quinolinate, the anion of quinolinic acid, also known as 2,3-pyridinedicarboxylic acid.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

21 records
Show feature table
Start End DB Term Name
21 281 Gene3D G3DSA:3.90.1170.20 -
21 281 InterPro IPR037128 Quinolinate phosphoribosyl transferase, N-terminal domain superfamily
126 278 Gene3D G3DSA:3.20.20.70 Aldolase class I
126 278 InterPro IPR013785 Aldolase-type TIM barrel
7 283 PANTHER PTHR32179 NICOTINATE-NUCLEOTIDE PYROPHOSPHORYLASE [CARBOXYLATING]
7 283 InterPro IPR027277 Nicotinate-nucleotide pyrophosphorylase/Putative pyrophosphorylase ModD
132 273 FunFam G3DSA:3.20.20.70:FF:000030 Nicotinate-nucleotide pyrophosphorylase, carboxylating
14 283 NCBIfam TIGR00078 carboxylating nicotinate-nucleotide diphosphorylase
14 283 InterPro IPR004393 Nicotinate-nucleotide pyrophosphorylase
21 128 FunFam G3DSA:3.90.1170.20:FF:000002 Nicotinate-nucleotide pyrophosphorylase [carboxylating]
3 117 SUPERFAMILY SSF54675 Nicotinate/Quinolinate PRTase N-terminal domain-like
4 284 PIRSF PIRSF006250 NadC_ModD
4 284 InterPro IPR027277 Nicotinate-nucleotide pyrophosphorylase/Putative pyrophosphorylase ModD
118 283 SUPERFAMILY SSF51690 Nicotinate/Quinolinate PRTase C-terminal domain-like
118 283 InterPro IPR036068 Nicotinate phosphoribosyltransferase-like, C-terminal
11 282 CDD cd01572 QPRTase
11 282 InterPro IPR004393 Nicotinate-nucleotide pyrophosphorylase
118 282 Pfam PF01729 Quinolinate phosphoribosyl transferase, C-terminal domain
118 282 InterPro IPR002638 Quinolinate phosphoribosyl transferase, C-terminal
30 116 Pfam PF02749 Quinolinate phosphoribosyl transferase, N-terminal domain
30 116 InterPro IPR022412 Quinolinate phosphoribosyl transferase, N-terminal

3D structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; AlphaFold DB and ColabFold models typically cover the full protein but remain computational predictions.

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Pocket score High Medium Low
How colors and pocket overlays are used
Uniform protein color marks the displayed model as a single molecular object.
Experimental PDB structures may be colored by chain to distinguish subunits or copies present in the file.
Pocket colors and alpha spheres are evidence overlays for predicted binding cavities; they are not alternative protein chains.
'Alpha spheres' is FPocket's own cavity-shape geometry, imported when available and aligned with the loaded structure.
'Pocket atoms'/'Predicted site atoms' show the pocket's residue atoms instead: P2Rank reports residues rather than alpha spheres, and FPocket falls back to this when alpha-sphere geometry is unavailable or doesn't align.
'No pocket geometry' means neither alpha spheres nor residue-position data could be found for that pocket; the layer just highlights the same residues as 'Nearby residues'.
Pocket details Inspect a specific pocket, or open the full viewer

Binding pockets · P2Rank

Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Pocket 1 P2Rank #1
0.583
Show in viewer
Surrounding area
Pocket 2 P2Rank #2
0.051
Show in viewer
Surrounding area
Pocket 3 P2Rank #3
0.023
Show in viewer
Surrounding area

Binding pockets · FPocket

Druggability (FPocket): high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Pocket 1 FPocket #3
0.283
Show in viewer
Surrounding area
Residue sets
UniProt: Binding site:119-119
UniProt: Binding site:152-154
UniProt: Binding site:176-176
UniProt: Binding site:186-186
UniProt: Binding site:215-215
UniProt: Binding site:236-236
UniProt: Binding site:259-261
UniProt: Binding site:280-282
All structural evidence 0 experimental · 2 predicted

Structural evidence

0 + 2

Experimental PDB entries plus predicted AlphaFold DB or ColabFold models. Click Switch to display a different loaded structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
AlphaFold DB AF_A0A0H3GJC5
AlphaFold DB full sequence Viewing
ColabFold KP13_01888
ColabFold full sequence Loaded

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.

54 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 4 records from similar proteins
Structural ligands 4 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
NCN PDB via homolog 335.2 Da · LogP -2.23 · TPSA 160.5 Open detail RCSB PDB
NTM PDB via homolog Detail RCSB PDB
PHT PDB via homolog Detail RCSB PDB
SRT PDB via homolog Detail RCSB PDB
ZINC4095572 ZINC proposed compound · Tanimoto 0.830 Detail ZINC

Structural evidence inferred from similar proteins. The source crystal indicates where the ligand was observed; the UniProt column identifies the homologous protein carrying that ligand.

Show only:
Ligand Source crystal UniProt (homolog) MW · LogP · TPSA Lipinski PAINS SMILES
NCN RCSB PDB I3LK75 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…
NTM RCSB PDB O25909 167.1 Da LogP 0.48 TPSA 87.5 ✓ Ro5 ✓ Clean c1cc(c(nc1)C(=O)O)C(=O)O
PHT RCSB PDB O25909 166.1 Da LogP 1.08 TPSA 74.6 ✓ Ro5 ✓ Clean c1ccc(c(c1)C(=O)O)C(=O)O
SRT RCSB PDB Q15274 150.1 Da LogP -2.12 TPSA 115.1 ✓ Ro5 ✓ Clean [C@H]([C@H](C(=O)O)O)(C(=O)O)O

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.

Cross-references

External database identifiers for this protein, its structures, ligands, and metabolic reactions.