Protein target profile

KP13_03261

Quinolinate synthase A

Genome: KpKP13 Gene: nadA AHE45640.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GU73
Length 348
Pocket druggability 0.87
Direct ligand evidence 0 72 total records
Functional annotation 1 EC 7 GO
Target summary

Promising target candidate with multiple supporting evidence streams.

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
No hit
Gut microbiome similarity
3.4% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
70.0 Higher values support similarity to known essential genes.
DEG E-value
1.24e-175 Smaller values mean stronger essential-gene similarity.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
93.15 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

The selected pocket score is the FPocket value used for ranking after applying the curated structure priority. It estimates small-molecule pocket quality; it is not experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

FPocket 0.87
Structure A0A0H3GU73
Pocket Pocket 17
P2Rank 0.889
Structure A0A0H3GU73
Pocket Pocket 1
ColabFold model
FPocket 0.955 · Pocket 1
P2Rank 0.913 · Pocket 1
Core conservation Accessory gene
Roary core
CoreCruncher accessory
Gut microbiome 163 / 4744 genomes with a hit
Prevalence 3.4%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MMSVMFDPETAIYPFPAKPQPLTVDEKQFYREKIKRLLRERDAVMVAHYYTDPEIQQLAEETGGCIADSLEMARFGARHSASTLLVAGVRFMGETAKILSPEKTILMPTLNAECSLDLGCPIEEFNAFCDAHPDRTVVVYANTSAAVKARADWVVTSSIAVELIDHLDSLGQKILWAPDRHLGRYVQRQTGADVLCWQGACIVHDEFKTQALMRMKALHPEAAVLVHPESPQAIVEMADAVGSTSQLIAAAKSLPQRQLIVATDRGIFYKMQQAVPEKTLLEAPTAGEGATCRSCAHCPWMAMNGLKAIAEGLEQGGAAHEIHIDEALRTGALIPLNRMLDFAATLRG

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:0008987 Catalysis of the reaction: iminoaspartate + dihydroxy-acetone-phosphate = quinolinate + 2 H2O + phosphate.
  • 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:0051539 Binding to a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
  • GO:0016765 Catalysis of the transfer of an alkyl or aryl (but not methyl) group from one compound (donor) to another (acceptor).
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0046872 Binding to a metal ion.
  • GO:0034628 The chemical reactions and pathways resulting in the formation of nicotinamide adenine dinucleotide (NAD+), beginning with the catabolism of L-aspartate into the precursor quinolinate. NAD+ is a coenzyme that interconverts with its reduced form, NADH, in many redox and catabolic reactions.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

17 records
Show feature table
Start End DB Term Name
28 342 NCBIfam TIGR00550 quinolinate synthase
28 342 InterPro IPR003473 Quinolinate synthetase A
201 296 Gene3D G3DSA:3.40.50.10800 -
201 296 InterPro IPR036094 Quinolinate synthetase A superfamily
33 323 Gene3D G3DSA:3.40.50.10800 -
33 323 InterPro IPR036094 Quinolinate synthetase A superfamily
286 345 PANTHER PTHR30573 QUINOLINATE SYNTHETASE A
286 345 InterPro IPR003473 Quinolinate synthetase A
116 216 FunFam G3DSA:3.40.50.10800:FF:000003 Quinolinate synthase A
116 340 Gene3D G3DSA:3.40.50.10800 -
116 340 InterPro IPR036094 Quinolinate synthetase A superfamily
30 342 SUPERFAMILY SSF142754 NadA-like
30 342 InterPro IPR036094 Quinolinate synthetase A superfamily
2 348 Hamap MF_00567 Quinolinate synthase [nadA].
2 348 InterPro IPR023513 Quinolinate synthase A, type 1
32 341 Pfam PF02445 Quinolinate synthetase A protein
32 341 InterPro IPR003473 Quinolinate synthetase A

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 · FPocket

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

Site 1 FPocket #17
0.87
Likely same site as P2Rank 4 1.9 Å 9 shared residues 100% of smaller site
Unusual size
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Surrounding area
Site 2 FPocket #2
0.632
Likely same site as P2Rank 1 0.8 Å 19 shared residues 100% of smaller site
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Surrounding area
Site 3 FPocket #1
0.28
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Surrounding area

Binding pockets · P2Rank

Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Site 1 P2Rank #1
0.889
Likely same site as FPocket 2 0.8 Å 19 shared residues 100% of smaller site
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Surrounding area
Site 2 P2Rank #2
0.072
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Surrounding area
Site 3 P2Rank #3
0.052
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Surrounding area
Site 4 P2Rank #4
0.037
Likely same site as FPocket 17 1.9 Å 9 shared residues 100% of smaller site
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Surrounding area
Site 5 P2Rank #5
0.031
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Surrounding area
Residue sets
UniProt: Binding site:114-114
UniProt: Binding site:140-142
UniProt: Binding site:157-157
UniProt: Binding site:201-201
UniProt: Binding site:227-229
UniProt: Binding site:244-244
UniProt: Binding site:298-298
UniProt: Binding site:48-48
UniProt: Binding site:69-69
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_A0A0H3GU73
AlphaFold DB full sequence Viewing
ColabFold KP13_03261
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.

72 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 22 records from similar proteins
Structural ligands 22 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
13P PDB via homolog 170.1 Da · LogP -1.34 · TPSA 104.1 Open detail RCSB PDB
5UK PDB via homolog Detail RCSB PDB
5XR PDB via homolog Detail RCSB PDB
5XW PDB via homolog Detail RCSB PDB
CIZ PDB via homolog Detail RCSB PDB

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
13P RCSB PDB O57767 170.1 Da LogP -1.34 TPSA 104.1 ✓ Ro5 ✓ Clean C(C(=O)COP(=O)(O)O)O
5UK RCSB PDB Q9X1X7 203.1 Da LogP -1.26 TPSA 135.8 ✓ Ro5 ✓ Clean [H]/N=C(\[C@H](CC(=O)CO)C(=O)O)/C(=O)O
5XR RCSB PDB O57767 221.2 Da LogP -2.27 TPSA 144.2 ✓ Ro5 ✓ Clean C(C=O)[C@@H](N[C@@](CC(=O)O)(C(=O)O)O)O
5XW RCSB PDB O57767 203.2 Da LogP -1.11 TPSA 124.3 ✓ Ro5 ✓ Clean C(C=O)C(/N=C(/CC(=O)O)\C(=O)O)O
CIZ RCSB PDB O57767 130.1 Da LogP 0.10 TPSA 74.6 ✓ Ro5 ✓ Clean C/C(=C/C(=O)O)/C(=O)O
DYA RCSB PDB O57767 131.1 Da LogP -1.00 TPSA 100.6 ✓ Ro5 ✓ Clean C(=C(/C(=O)O)\N)\C(=O)O
FLC RCSB PDB Q9X1X7 189.1 Da LogP -5.25 TPSA 140.6 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[O-])O
GZ8 RCSB PDB Q9X1X7 198.2 Da LogP 0.64 TPSA 74.6 ✓ Ro5 Alert C1=CC(=S)C=C(C1C(=O)O)C(=O)O
H2S RCSB PDB Q9X1X7 34.1 Da LogP 0.11 TPSA 0.0 ✓ Ro5 ✓ Clean S
ITN RCSB PDB O57767 130.1 Da LogP 0.10 TPSA 74.6 ✓ Ro5 ✓ Clean C=C(CC(=O)O)C(=O)O
LMR RCSB PDB O57767 134.1 Da LogP -1.09 TPSA 94.8 ✓ Ro5 ✓ Clean C([C@@H](C(=O)O)O)C(=O)O
MAE RCSB PDB O57767 116.1 Da LogP -0.29 TPSA 74.6 ✓ Ro5 ✓ Clean C(=C/C(=O)O)/C(=O)O
MLT RCSB PDB O57767 134.1 Da LogP -1.09 TPSA 94.8 ✓ Ro5 ✓ Clean C([C@H](C(=O)O)O)C(=O)O
NH4 RCSB PDB O57767 18.0 Da LogP 0.38 TPSA 36.5 ✓ Ro5 ✓ Clean [NH4+]
NHE RCSB PDB Q9X1X7 207.3 Da LogP 0.80 TPSA 66.4 ✓ Ro5 ✓ Clean C1CCC(CC1)NCCS(=O)(=O)O
NTM RCSB PDB Q9X1X7 167.1 Da LogP 0.48 TPSA 87.5 ✓ Ro5 ✓ Clean c1cc(c(nc1)C(=O)O)C(=O)O
PGH RCSB PDB Q9X1X7 171.0 Da LogP -1.40 TPSA 116.1 ✓ Ro5 ✓ Clean C(C(=O)NO)OP(=O)(O)O
PHT RCSB PDB Q9X1X7 166.1 Da LogP 1.08 TPSA 74.6 ✓ Ro5 ✓ Clean c1ccc(c(c1)C(=O)O)C(=O)O
QAS RCSB PDB Q9X1X7 199.2 Da LogP 0.77 TPSA 87.5 ✓ Ro5 ✓ Clean c1cc(nc(c1C(=O)O)C(=O)O)S
QAT RCSB PDB Q9X1X7 199.2 Da LogP 0.25 TPSA 87.0 ✓ Ro5 Alert C1C(=S)C=NC(=C1C(=O)O)C(=O)O
XQB RCSB PDB Q9X1X7 203.1 Da LogP -1.26 TPSA 135.8 ✓ Ro5 ✓ Clean [H]/N=C(/[C@H](C[C@@H](C=O)O)C(=O)O)\C(=O)O
YQA RCSB PDB Q9X1X7 185.1 Da LogP -0.75 TPSA 107.2 ✓ Ro5 ✓ Clean C1[C@H](C=NC(=C1C(=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.