KpKP13 Protein target profile
Nicotinate-nucleotide pyrophosphorylase carboxylating
Accession: KP13_01888
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.
Main supporting evidence
Risks to review
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 modelP2Rank'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.
Sequence
Primary amino-acid sequence viewer.
MLLERINLDITDAVAHSLREDLGGEVDANNDISAQLLPQDARSHAVVITREDGVFCGKRWVEEVFIQLAGDDVNITWHVADGDAVKADQPLFELEGPSRILLTGERTALNFVQTLSGVASVVRRYVDLLAGTKTQLLDTRKTLPGLRTALKYAVLCGGGANHRLGLFDAFLIKENHIIASGSIRQAVEKAFWLHPDVPVEVEVETLDELEQALKAGADIIMLDNFTTDLMREAVKITAGQAALEVSGNVTFDTIREFADTGVDYISVGALTKHVQALDLSMRFR
Functional annotations
Enzyme classification and Gene Ontology terms linked to this protein.
Subcellular localization
- Localization
- Cytoplasmic
Enzyme Commission (EC)
1Gene 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.
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.
How colors and pocket overlays are used
Pocket details Inspect a specific pocket, or open the full viewer
- Method
- -
- Score
- -
- Visible layer
- -
- Residues
- -
- Pocket properties
- -
Selecting a pocket opens its details and centers the viewer without clearing other active layers. Use Focus this pocket when you want to hide the rest; use Surface for the wider residue environment.
Binding pockets · P2Rank
Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2
Binding pockets · FPocket
Druggability (FPocket): high ≥ 0.7 · medium 0.4–0.69 · low < 0.4
Residue sets
Binding pockets · P2Rank
Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2
Binding pockets · FPocket
Druggability (FPocket): high ≥ 0.7 · medium 0.4–0.69 · low < 0.4
All structural evidence
Structural evidence
0 + 2Experimental 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.
Structural ligand evidence is available for this target.
Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in Target, use Open crystal to inspect it in the structure viewer.
No PDB structure with a co-crystallized ligand found for this exact protein.
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.
| 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
|
Experimental bioactivity from ChEMBL measured directly on this protein. Score = pchembl (−log Ki/IC₅₀; higher = more potent).
No ChEMBL bioactivity data found for this exact protein.
Bioactivity inferred from similar proteins in ChEMBL. Score = pchembl (−log Ki/IC₅₀; higher = more potent).
No ChEMBL hits found through similar proteins.
Proposed virtual-screening candidates from ZINC. Score = Tanimoto similarity to a known binder (0–1; higher = more similar).
| Ligand | Tanimoto | MW · LogP · TPSA | Lipinski | PAINS | SMILES |
|---|---|---|---|---|---|
| ZINC4095572 ZINC | 0.830 | 336.2 Da LogP -1.60 TPSA 157.6 | ✓ Ro5 | ✓ Clean |
O=C(O)c1ccc[n+]([C@@H]2O[C@H](COP(=O)(O)O)[C@@H…
|
| ZINC77311659 ZINC | 0.830 | 336.2 Da LogP -1.60 TPSA 157.6 | ✓ Ro5 | ✓ Clean |
O=C(O)c1ccc[n+]([C@@H]2O[C@H](COP(=O)(O)O)[C@H]…
|
| ZINC77311660 ZINC | 0.830 | 336.2 Da LogP -1.60 TPSA 157.6 | ✓ Ro5 | ✓ Clean |
O=C(O)c1ccc[n+]([C@@H]2O[C@H](COP(=O)(O)O)[C@H]…
|
| ZINC77311661 ZINC | 0.830 | 336.2 Da LogP -1.60 TPSA 157.6 | ✓ Ro5 | ✓ Clean |
O=C(O)c1ccc[n+]([C@@H]2O[C@H](COP(=O)(O)O)[C@@H…
|
| ZINC105146 ZINC | 0.722 | 242.2 Da LogP 2.75 TPSA 74.6 | ✓ Ro5 | ✓ Clean |
O=C(O)c1ccccc1-c1ccccc1C(=O)O
|
| ZINC157193 ZINC | 0.700 | 226.2 Da LogP 2.62 TPSA 54.4 | ✓ Ro5 | ✓ Clean |
O=C(O)c1ccccc1C(=O)c1ccccc1
|
| ZINC1604722 ZINC | 0.700 | 326.3 Da LogP 2.93 TPSA 108.7 | ✓ Ro5 | ✓ Clean |
O=C(O)c1ccccc1C(=O)CCC(=O)c1ccccc1C(=O)O
|
| ZINC12359024 ZINC | 0.692 | 210.1 Da LogP -3.40 TPSA 155.5 | 1 viol. | ✓ Clean |
O=C(O)[C@@H](O)[C@H](O)[C@H](O)[C@@H](O)C(=O)O
|
| ZINC13533920 ZINC | 0.692 | 210.1 Da LogP -3.40 TPSA 155.5 | 1 viol. | ✓ Clean |
O=C(O)[C@@H](O)[C@H](O)[C@@H](O)[C@@H](O)C(=O)O
|
| ZINC1532740 ZINC | 0.692 | 210.1 Da LogP -3.40 TPSA 155.5 | 1 viol. | ✓ Clean |
O=C(O)[C@@H](O)[C@H](O)[C@@H](O)[C@H](O)C(=O)O
|
| ZINC1549593 ZINC | 0.692 | 210.1 Da LogP -3.40 TPSA 155.5 | 1 viol. | ✓ Clean |
O=C(O)[C@H](O)[C@H](O)[C@@H](O)[C@@H](O)C(=O)O
|
| ZINC2013424 ZINC | 0.692 | 210.1 Da LogP -3.40 TPSA 155.5 | 1 viol. | ✓ Clean |
O=C(O)[C@@H](O)[C@@H](O)[C@@H](O)[C@H](O)C(=O)O
|
| ZINC3581021 ZINC | 0.692 | 210.1 Da LogP -3.40 TPSA 155.5 | 1 viol. | ✓ Clean |
O=C(O)[C@H](O)[C@@H](O)[C@@H](O)[C@@H](O)C(=O)O
|
| ZINC3860635 ZINC | 0.692 | 210.1 Da LogP -3.40 TPSA 155.5 | 1 viol. | ✓ Clean |
O=C(O)[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)C(=O)O
|
| ZINC5783661 ZINC | 0.692 | 210.1 Da LogP -3.40 TPSA 155.5 | 1 viol. | ✓ Clean |
O=C(O)[C@@H](O)[C@@H](O)[C@H](O)[C@@H](O)C(=O)O
|
| ZINC6072527 ZINC | 0.692 | 210.1 Da LogP -3.40 TPSA 155.5 | 1 viol. | ✓ Clean |
O=C(O)[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)C(=O)O
|
| ZINC135598 ZINC | 0.690 | 227.2 Da LogP 2.01 TPSA 67.3 | ✓ Ro5 | ✓ Clean |
O=C(c1ccccc1)c1cccnc1C(=O)O
|
| ZINC343335 ZINC | 0.690 | 227.2 Da LogP 2.01 TPSA 67.3 | ✓ Ro5 | ✓ Clean |
O=C(O)c1cccnc1C(=O)c1ccccc1
|
| ZINC12503278 ZINC | 0.673 | 335.2 Da LogP -2.20 TPSA 163.4 | ✓ Ro5 | ✓ Clean |
NC(=O)c1ccc[n+]([C@@H]2O[C@H](COP(=O)(O)O)[C@@H…
|
| ZINC1532667 ZINC | 0.673 | 335.2 Da LogP -2.20 TPSA 163.4 | ✓ Ro5 | ✓ Clean |
NC(=O)c1ccc[n+]([C@H]2O[C@@H](COP(=O)(O)O)[C@H]…
|
| ZINC2545161 ZINC | 0.673 | 335.2 Da LogP -2.20 TPSA 163.4 | ✓ Ro5 | ✓ Clean |
NC(=O)c1ccc[n+]([C@@H]2O[C@@H](COP(=O)(O)O)[C@H…
|
| ZINC3870109 ZINC | 0.673 | 335.2 Da LogP -2.20 TPSA 163.4 | ✓ Ro5 | ✓ Clean |
NC(=O)c1ccc[n+]([C@@H]2O[C@@H](COP(=O)(O)O)[C@@…
|
| ZINC40465856 ZINC | 0.673 | 335.2 Da LogP -2.20 TPSA 163.4 | ✓ Ro5 | ✓ Clean |
NC(=O)c1ccc[n+]([C@@H]2O[C@H](COP(=O)(O)O)[C@H]…
|
| ZINC40762833 ZINC | 0.673 | 335.2 Da LogP -2.20 TPSA 163.4 | ✓ Ro5 | ✓ Clean |
NC(=O)c1ccc[n+]([C@H]2O[C@H](COP(=O)(O)O)[C@@H]…
|
| ZINC4228273 ZINC | 0.673 | 335.2 Da LogP -2.20 TPSA 163.4 | ✓ Ro5 | ✓ Clean |
NC(=O)c1ccc[n+]([C@@H]2O[C@H](COP(=O)(O)O)[C@@H…
|
| ZINC77311638 ZINC | 0.673 | 335.2 Da LogP -2.20 TPSA 163.4 | ✓ Ro5 | ✓ Clean |
NC(=O)c1ccc[n+]([C@@H]2O[C@H](COP(=O)(O)O)[C@H]…
|
| ZINC1600331 ZINC | 0.667 | 330.2 Da LogP 2.15 TPSA 149.2 | ✓ Ro5 | ✓ Clean |
O=C(O)c1cccc(C(=O)O)c1-c1c(C(=O)O)cccc1C(=O)O
|
| ZINC1296728 ZINC | 0.654 | 244.2 Da LogP 1.54 TPSA 100.4 | ✓ Ro5 | ✓ Clean |
O=C(O)c1ncccc1-c1cccnc1C(=O)O
|
| ZINC47217 ZINC | 0.654 | 244.2 Da LogP 1.54 TPSA 100.4 | ✓ Ro5 | ✓ Clean |
O=C(O)c1cccnc1-c1ncccc1C(=O)O
|
| ZINC164706 ZINC | 0.650 | 201.0 Da LogP 2.15 TPSA 37.3 | ✓ Ro5 | ✓ Clean |
O=C(O)c1ccccc1Br
|
| ZINC90931 ZINC | 0.650 | 248.0 Da LogP 1.99 TPSA 37.3 | ✓ Ro5 | ✓ Clean |
O=C(O)c1ccccc1I
|
| ZINC4096931 ZINC | 0.646 | 256.2 Da LogP -1.72 TPSA 111.1 | ✓ Ro5 | ✓ Clean |
O=C(O)c1ccc[n+]([C@@H]2O[C@H](CO)[C@@H](O)[C@H]…
|
| ZINC343704 ZINC | 0.636 | 208.2 Da LogP 1.04 TPSA 91.7 | ✓ Ro5 | ✓ Clean |
O=C(O)CC(=O)c1ccccc1C(=O)O
|
| ZINC39055766 ZINC | 0.636 | 218.1 Da LogP 2.13 TPSA 54.4 | ✓ Ro5 | ✓ Clean |
O=C(O)c1ccccc1C(=O)C(F)(F)F
|
| ZINC394370 ZINC | 0.636 | 270.2 Da LogP 2.31 TPSA 91.7 | ✓ Ro5 | ✓ Clean |
O=C(O)c1ccc(C(=O)c2ccccc2C(=O)O)cc1
|
| ZINC4394109 ZINC | 0.636 | 382.4 Da LogP 1.68 TPSA 115.2 | ✓ Ro5 | ✓ Clean |
O=C(O)c1ccccc1C(=O)N1CCN(C(=O)c2ccccc2C(=O)O)CC1
|
| ZINC388710 ZINC | 0.632 | 210.1 Da LogP 0.78 TPSA 111.9 | ✓ Ro5 | ✓ Clean |
O=C(O)c1cccc(C(=O)O)c1C(=O)O
|
| ZINC389564 ZINC | 0.632 | 216.2 Da LogP 2.24 TPSA 74.6 | ✓ Ro5 | ✓ Clean |
O=C(O)c1ccc(C(=O)O)c2ccccc12
|
| ZINC45070868 ZINC | 0.632 | 216.2 Da LogP 2.24 TPSA 74.6 | ✓ Ro5 | ✓ Clean |
O=C(O)c1cccc2c(C(=O)O)cccc12
|
| ZINC391925 ZINC | 0.625 | 254.1 Da LogP 0.48 TPSA 149.2 | ✓ Ro5 | ✓ Clean |
O=C(O)c1cc(C(=O)O)c(C(=O)O)cc1C(=O)O
|
| ZINC154566 ZINC | 0.619 | 257.2 Da LogP 2.83 TPSA 86.6 | ✓ Ro5 | ✓ Clean |
O=C(O)c1ccccc1Nc1ccccc1C(=O)O
|
| ZINC256346309 ZINC | 0.619 | 270.2 Da LogP 3.50 TPSA 99.3 | ✓ Ro5 | Alert |
O=C(O)c1ccccc1N=Nc1ccccc1C(=O)O
|
| ZINC3845505 ZINC | 0.619 | 268.3 Da LogP 3.25 TPSA 74.6 | ✓ Ro5 | ✓ Clean |
O=C(O)c1ccccc1/C=C/c1ccccc1C(=O)O
|
| ZINC410108 ZINC | 0.619 | 258.2 Da LogP 2.88 TPSA 83.8 | ✓ Ro5 | ✓ Clean |
O=C(O)c1ccccc1Oc1ccccc1C(=O)O
|
| ZINC5369059 ZINC | 0.619 | 274.3 Da LogP 3.23 TPSA 74.6 | ✓ Ro5 | ✓ Clean |
O=C(O)c1ccccc1Sc1ccccc1C(=O)O
|
| ZINC5771961 ZINC | 0.619 | 256.3 Da LogP 2.67 TPSA 74.6 | ✓ Ro5 | ✓ Clean |
O=C(O)c1ccccc1Cc1ccccc1C(=O)O
|
| ZINC62723773 ZINC | 0.619 | 270.2 Da LogP 3.50 TPSA 99.3 | ✓ Ro5 | Alert |
O=C(O)c1ccccc1/N=N/c1ccccc1C(=O)O
|
| ZINC3843351 ZINC | 0.609 | 358.3 Da LogP 2.10 TPSA 127.2 | ✓ Ro5 | ✓ Clean |
O=C(O)c1ccccc1C(=O)OCCOC(=O)c1ccccc1C(=O)O
|
| ZINC4178076 ZINC | 0.609 | 404.4 Da LogP 3.59 TPSA 132.8 | ✓ Ro5 | ✓ Clean |
O=C(O)c1ccccc1C(=O)Nc1ccccc1NC(=O)c1ccccc1C(=O)O
|
| ZINC518924 ZINC | 0.609 | 284.3 Da LogP 2.51 TPSA 91.7 | ✓ Ro5 | ✓ Clean |
O=C(O)c1ccccc1CC(=O)c1ccccc1C(=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.