KpKP13 Protein target profile

Phosphoribosylglycinamide formyltransferase 2

Accession: KP13_01608

Gene: AHE43869.1 purT 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GQ50
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Length 392
Pocket druggability (P2Rank · AlphaFold DB model) 0.967
Direct ligand evidence 0 58 total records
Functional annotation 1 EC 9 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.

Main supporting evidence

No similar human protein detected The current BLAST sequence screen did not find a significant human match, lowering apparent off-target risk. Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Second pocket predictor agrees P2Rank predicted binding-site probability 0.97. Structure available AlphaFold DB model + ColabFold model Review the complete evidence below

Risks to review

Microbiome similarity 626 of 4744 screened genomes (13.2%) have a significant similarity hit. This target also has a predicted binding pocket (P2Rank 0.97) — check the ligand evidence before deprioritizing on off-target risk alone. Weak predicted binding pocket FPocket selected-pocket score 0.36.

Evidence gaps

No metabolic context No SBML/network-derived reaction evidence is loaded for 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
13.2% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
N
DEG identity (%)
0.0 Higher values support similarity to known essential genes.

Structure confidence

ColabFold pLDDT
97.08 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) 0.967
Structure A0A0H3GQ50
Pocket Pocket 1
Druggability (FPocket) 0.36
Structure A0A0H3GQ50
Pocket Pocket 1
ColabFold model
P2Rank 0.968 · Pocket 1
FPocket 0.175 · Pocket 5
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 626 / 4744 genomes with a hit
Prevalence 13.2%

Sequence

Primary amino-acid sequence viewer.

MTVLGTALRPAATKVMLLGSGELGKEVAIECQRLGIETIAVDRYPDAPAMQVAHRAHVINMLHGESLRALIEQEKPDYIVPEIEAIATDTLVELEQAGQKVVPTARAAKLTMNREGIRRLAAEELQLPTSRYRFADSEEGFRAAVTEIGLPCIVKPVMSSSGKGQSFIRSADQLSEAWRYAQQGGRAGAGRVIVEGVVNFDFEITLLTVSAVDGVHFCAPVGHRQEDGDYRESWQPQQMSDLALERAQTIARKVVLALGGYGLFGVELFVCGDEVIFSEVSPRPHDTGMVTLISQDLSEFALHVRAFLGLPVGAIRQYGPAASAVILPQLSSQNVSFGQLQSAVGAGLQLRLFGKPEIDGTRRLGVTLAVADSVEEAVARAKAAAAAVIVEG

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 9 GO

Subcellular localization

Localization
CytoplasmicMembrane

Enzyme Commission (EC)

1

Gene Ontology (GO)

9
  • GO:0009152 The chemical reactions and pathways resulting in the formation of a purine ribonucleotide, a compound consisting of ribonucleoside (a purine base linked to a ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
  • GO:0046872 Binding to a metal ion.
  • GO:0004644 Catalysis of the reaction: 10-formyltetrahydrofolate + N1-(5-phospho-D-ribosyl)glycinamide = tetrahydrofolate + N2-formyl-N1-(5-phospho-D-ribosyl)glycinamide.
  • GO:0000287 Binding to a magnesium (Mg) ion.
  • GO:0016742 Catalysis of the transfer of a hydroxymethyl- or formyl group from one compound (donor) to another (acceptor).
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0043815 Catalysis of the reaction: ATP + formate + N1-(5-phospho-beta-D-ribosyl)glycinamide = ADP + H+ + N2-formyl-N1-(5-phospho-beta-D-ribosyl)glycinamide + phosphate.
  • GO:0006189 The chemical reactions and pathways resulting in the formation of IMP, inosine monophosphate, by the stepwise assembly of a purine ring on ribose 5-phosphate.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

21 records
Show feature table
Start End DB Term Name
14 390 NCBIfam TIGR01142 phosphoribosylglycinamide formyltransferase 2
14 390 InterPro IPR005862 Formate-dependent phosphoribosylglycinamide formyltransferase
8 391 Hamap MF_01643 Formate-dependent phosphoribosylglycinamide formyltransferase [purT].
8 391 InterPro IPR005862 Formate-dependent phosphoribosylglycinamide formyltransferase
319 391 SUPERFAMILY SSF51246 Rudiment single hybrid motif
319 391 InterPro IPR011054 Rudiment single hybrid motif
197 390 FunFam G3DSA:3.30.470.20:FF:000027 Formate-dependent phosphoribosylglycinamide formyltransferase
2 123 FunFam G3DSA:3.40.50.20:FF:000007 Formate-dependent phosphoribosylglycinamide formyltransferase
119 308 ProSiteProfiles PS50975 ATP-grasp fold profile.
119 308 InterPro IPR011761 ATP-grasp fold
3 112 SUPERFAMILY SSF52440 PreATP-grasp domain
3 112 InterPro IPR016185 Pre-ATP-grasp domain superfamily
123 196 Gene3D G3DSA:3.30.1490.20 -
123 196 InterPro IPR013815 ATP-grasp fold, subdomain 1
124 196 FunFam G3DSA:3.30.1490.20:FF:000013 Formate-dependent phosphoribosylglycinamide formyltransferase
113 314 SUPERFAMILY SSF56059 Glutathione synthetase ATP-binding domain-like
197 390 Gene3D G3DSA:3.30.470.20 -
123 294 Pfam PF02222 ATP-grasp domain
123 294 InterPro IPR003135 ATP-grasp fold, ATP-dependent carboxylate-amine ligase-type
2 122 Gene3D G3DSA:3.40.50.20 -
1 391 PANTHER PTHR43055 FORMATE-DEPENDENT PHOSPHORIBOSYLGLYCINAMIDE FORMYLTRANSFERASE

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
0.967
Show in viewer
Surrounding area
Pocket 2 P2Rank #2
0.008
Show in viewer
Surrounding area
Pocket 3 P2Rank #3
0.006
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #1
0.36
Show in viewer
Surrounding area
Residue sets
UniProt: Binding site:114-114
UniProt: Binding site:155-155
UniProt: Binding site:160-165
UniProt: Binding site:195-198
UniProt: Binding site:203-203
UniProt: Binding site:22-23
UniProt: Binding site:267-267
UniProt: Binding site:279-279
UniProt: Binding site:286-286
UniProt: Binding site:355-355
UniProt: Binding site:362-363
UniProt: Binding site:82-82
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_A0A0H3GQ50
AlphaFold DB — — full sequence — Viewing
ColabFold KP13_01608
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.

58 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 8 records from similar proteins
Structural ligands 8 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
A12 PDB via homolog 425.2 Da · LogP -1.64 · TPSA 223.4 Open detail RCSB PDB
ACP PDB via homolog Detail RCSB PDB
AGS PDB via homolog Detail RCSB PDB
AIR PDB via homolog Detail RCSB PDB
ANP 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
A12 RCSB PDB
4MAM
Q5NGE8 425.2 Da LogP -1.64 TPSA 223.4 2 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
ACP RCSB PDB
1KJI
P33221 505.2 Da LogP -1.52 TPSA 269.9 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
AGS RCSB PDB
1KJJ
P33221 523.2 Da LogP -1.51 TPSA 262.1 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
AIR RCSB PDB
3K5I
A1CII2 295.2 Da LogP -1.81 TPSA 160.3 ✓ Ro5 ✓ Clean c1c(n(cn1)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(…
ANP RCSB PDB
1EYZ
P33221 506.2 Da LogP -2.06 TPSA 281.9 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
GAR RCSB PDB
1EZ1
P33221 284.2 Da LogP -4.65 TPSA 177.2 ✓ Ro5 ✓ Clean C([C@@H]1[C@H]([C@H]([C@@H](O1)NC(=O)CN)O)O)OP(…
NHE RCSB PDB
3K5I
A1CII2 207.3 Da LogP 0.80 TPSA 66.4 ✓ Ro5 ✓ Clean C1CCC(CC1)NCCS(=O)(=O)O
POP RCSB PDB
3ORQ
A0A0H3KFM7 176.0 Da LogP -2.08 TPSA 129.9 ✓ Ro5 ✓ Clean O[P@@](=O)([O-])O[P@@](=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.

Sequence

UniProt A0A0H3GQ50