Protein target profile

KP13_03811

Phosphoribosylglycinamide formyltransferase

Genome: KpKP13 Gene: purN AHE43296.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GWL7
Length 213
Pocket druggability 0.601
Direct ligand evidence 0 147 total records
Functional annotation 1 EC 4 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
Hit
Human identity (%)
43.972 Lower values reduce human off-target concern.
Human E-value
1.92e-35
Gut microbiome similarity
3.8% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
58.373 Higher values support similarity to known essential genes.
DEG E-value
1.73e-85 Smaller values mean stronger essential-gene similarity.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
96.79 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 0.601
Structure A0A0H3GWL7
Pocket Pocket 2
P2Rank 0.894
Structure A0A0H3GWL7
Pocket Pocket 1
ColabFold model
FPocket 0.26 · Pocket 2
P2Rank 0.865 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 178 / 4744 genomes with a hit
Prevalence 3.8%

Cross-references

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

Chemistry

ChEMBL CHEMBL279302 ChEMBL CHEMBL607957 ChEMBL CHEMBL4643623 ChEMBL CHEMBL4465095 ChEMBL CHEMBL4636872 ChEMBL CHEMBL192632 ChEMBL CHEMBL4538151 ChEMBL CHEMBL4445651 ChEMBL CHEMBL4214638 ChEMBL CHEMBL4557278 ChEMBL CHEMBL82261 ChEMBL CHEMBL4471269 ChEMBL CHEMBL4645676 ChEMBL CHEMBL85436 ChEMBL CHEMBL82181 ChEMBL CHEMBL4205344 ChEMBL CHEMBL4553188 ChEMBL CHEMBL4467936 ChEMBL CHEMBL4638232 ChEMBL CHEMBL4444011 ChEMBL CHEMBL4447805 ChEMBL CHEMBL502528 ChEMBL CHEMBL526928 ChEMBL CHEMBL84935 ChEMBL CHEMBL3086867 ChEMBL CHEMBL267890 ChEMBL LYA ChEMBL CHEMBL3335605 ChEMBL CHEMBL4641908 ChEMBL CHEMBL490934 ChEMBL CHEMBL451819 ChEMBL CHEMBL84605 ChEMBL CHEMBL451818 ChEMBL CHEMBL82390 ChEMBL CHEMBL350097 ChEMBL CHEMBL491129 ChEMBL CHEMBL491298 ChEMBL CHEMBL84163 ChEMBL CHEMBL309415 ChEMBL CHEMBL379094 ChEMBL CHEMBL315627 ChEMBL CHEMBL522455 ChEMBL CHEMBL315076 ChEMBL CHEMBL85871 ChEMBL CHEMBL84904 ChEMBL CHEMBL4642637 ChEMBL CHEMBL38902 ChEMBL DDF ChEMBL CHEMBL3409335 ChEMBL CHEMBL279508 ChEMBL CHEMBL314116 ChEMBL CHEMBL3628345 ChEMBL CHEMBL3628347 ChEMBL CHEMBL170101 ChEMBL CHEMBL424683 ChEMBL CHEMBL294768 ChEMBL CHEMBL3085263 ChEMBL 3Y9 ChEMBL DXY ChEMBL CHEMBL417696 ChEMBL CHEMBL5417651 ChEMBL CHEMBL5429283 ChEMBL CHEMBL5438587 ChEMBL CHEMBL257691 ChEMBL CHEMBL66389 ChEMBL CHEMBL84045 ChEMBL CHEMBL452324 ChEMBL CHEMBL2107361 ChEMBL CHEMBL2360464 ChEMBL CHEMBL3989962 ChEMBL CHEMBL4435608 ChEMBL CHEMBL4515056 ChEMBL CHEMBL5315053 ChEMBL CHEMBL6068329

Sequence

Primary amino-acid sequence viewer.

MKNIVVLISGSGSNLQAIIDACGRKQINGTLRAVFSNKADAFGLERARLAGIPAHALAQSQFADREAFDRQLMHEIDAYGPDLVVLAGYMRILSPAFVSHYQGRLLNIHPSLLPKYPGLHTHRQVLENGDEEHGTSVHFVTDELDGGPVILQAKVPVFAGDSEEEITARVQAQEHAIYPLVISWFVDGRLRMAGNHAWLDERQLPPQGYAADE

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

4
  • 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.
  • 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.
  • GO:0004644 Catalysis of the reaction: 10-formyltetrahydrofolate + N1-(5-phospho-D-ribosyl)glycinamide = tetrahydrofolate + N2-formyl-N1-(5-phospho-D-ribosyl)glycinamide.
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

20 records
Show feature table
Start End DB Term Name
2 204 SUPERFAMILY SSF53328 Formyltransferase
2 204 InterPro IPR036477 Formyl transferase, N-terminal domain superfamily
4 12 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
3 188 Hamap MF_01930 Phosphoribosylglycinamide formyltransferase [purN].
3 188 InterPro IPR004607 Phosphoribosylglycinamide formyltransferase
13 17 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
1 3 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
3 185 CDD cd08645 FMT_core_GART
3 185 InterPro IPR004607 Phosphoribosylglycinamide formyltransferase
134 157 ProSitePatterns PS00373 Phosphoribosylglycinamide formyltransferase active site.
134 157 InterPro IPR001555 Phosphoribosylglycinamide formyltransferase, active site
2 182 Pfam PF00551 Formyl transferase
2 182 InterPro IPR002376 Formyl transferase, N-terminal
2 213 FunFam G3DSA:3.40.50.170:FF:000005 Phosphoribosylglycinamide formyltransferase
2 192 NCBIfam TIGR00639 phosphoribosylglycinamide formyltransferase
2 192 InterPro IPR004607 Phosphoribosylglycinamide formyltransferase
1 17 Phobius SIGNAL_PEPTIDE Signal peptide region
2 213 Gene3D G3DSA:3.40.50.170 -
2 199 PANTHER PTHR43369 PHOSPHORIBOSYLGLYCINAMIDE FORMYLTRANSFERASE
18 213 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.

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.

Download VMD script Full viewer

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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 #2
0.601
Likely same site as P2Rank 1 1.3 Å 26 shared residues 100% of smaller site
Unusual size
Show in viewer
Surrounding area

Binding pockets · P2Rank

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

Site 1 P2Rank #1
0.894
Likely same site as FPocket 2 1.3 Å 26 shared residues 100% of smaller site
Show in viewer
Surrounding area
Residue sets
UniProt: Active site:109-109 Proton donor
UniProt: Binding site:107-107
UniProt: Binding site:12-14
UniProt: Binding site:65-65
UniProt: Binding site:90-93
UniProt: Site:145-145 Raises pKa of active site His
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_A0A0H3GWL7
AlphaFold DB full sequence Viewing
ColabFold KP13_03811
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.

147 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 97 records from similar proteins
Structural ligands 23 0 loaded crystals
Measured bioactivity 74 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
138 PDB via homolog 752.6 Da · LogP -2.34 · TPSA 353.5 Open detail RCSB PDB
3YA PDB via homolog Detail RCSB PDB
3YB PDB via homolog Detail RCSB PDB
3YC PDB via homolog Detail RCSB PDB
3YD 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
138 RCSB PDB P08179 752.6 Da LogP -2.34 TPSA 353.5 3 viol. ✓ Clean c1cc(ccc1C(=O)N[C@@H](CCC(=O)O)C(=O)O)[C@@](Cc2…
3YA RCSB PDB P22102 472.5 Da LogP 2.18 TPSA 175.5 ✓ Ro5 ✓ Clean c1cc(ccc1CCCCc2cc3c(s2)NC(=NC3=O)N)C(=O)N[C@@H]…
3YB RCSB PDB P22102 461.5 Da LogP 1.51 TPSA 191.3 1 viol. ✓ Clean c1c(csc1C(=O)N[C@@H](CCC(=O)O)C(=O)O)CCCCc2cc3c…
3YC RCSB PDB P22102 461.5 Da LogP 1.51 TPSA 191.3 1 viol. ✓ Clean c1c(csc1CCCCc2cc3c([nH]2)N=C(NC3=O)N)C(=O)N[C@@…
3YD RCSB PDB P22102 407.4 Da LogP 0.76 TPSA 191.3 1 viol. ✓ Clean c1c([nH]c2c1C(=O)NC(=N2)N)CCCCCCC(=O)N[C@@H](CC…
3YE RCSB PDB P22102 421.5 Da LogP 1.15 TPSA 191.3 1 viol. ✓ Clean c1c([nH]c2c1C(=O)NC(=N2)N)CCCCCCCC(=O)N[C@@H](C…
3YF RCSB PDB P22102 447.5 Da LogP 1.12 TPSA 191.3 1 viol. ✓ Clean c1c(csc1C(=O)N[C@@H](CCC(=O)O)C(=O)O)CCCc2cc3c(…
3YG RCSB PDB P22102 447.5 Da LogP 1.12 TPSA 191.3 1 viol. ✓ Clean c1c(csc1CCCc2cc3c([nH]2)N=C(NC3=O)N)C(=O)N[C@@H…
4DW RCSB PDB P22102 425.4 Da LogP 0.44 TPSA 191.3 1 viol. ✓ Clean c1cc(ccc1CCc2c[nH]c3c2C(=O)N=C(N3)N)C(=O)N[C@@H…
83A RCSB PDB P22102 442.4 Da LogP 0.54 TPSA 203.3 1 viol. ✓ Clean c1cc(ccc1C(=O)N[C@@H](CCC(=O)O)C(=O)O)NCCc2cc3c…
DXZ RCSB PDB P22102 477.5 Da LogP 1.41 TPSA 201.5 1 viol. ✓ Clean CS[C@H](CCCC1=C(N=C(NC1=O)N)N)c2ccc(cc2)C(=O)N[…
DZF RCSB PDB P08179 440.4 Da LogP 0.56 TPSA 200.4 1 viol. ✓ Clean c1cc(ccc1C(=O)N[C@@H](CCC(=O)O)C(=O)O)NCc2cc3c(…
G71 RCSB PDB P22102 461.5 Da LogP 1.51 TPSA 191.3 1 viol. ✓ Clean c1cc(sc1CCCCc2cc3c([nH]2)NC(=NC3=O)N)C(=O)N[C@@…
G94 RCSB PDB P22102 447.5 Da LogP 1.12 TPSA 191.3 1 viol. ✓ Clean c1cc(sc1CCCc2cc3c([nH]2)NC(=NC3=O)N)C(=O)N[C@@H…
GAR RCSB PDB P22102 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(…
KEU RCSB PDB P22102 549.5 Da LogP -0.91 TPSA 237.3 2 viol. ✓ Clean c1cc(ccc1[C@@H](CCCC2C(NC(NC2=O)N)N)C(C(F)(F)F)…
KT3 RCSB PDB P22102 803.7 Da LogP -0.56 TPSA 375.0 3 viol. ✓ Clean c1cc(ccc1[C@H](CCCc2c(nc(nc2O)N)N)C(C(F)(F)F)(O…
KT5 RCSB PDB P22102 1061.9 Da LogP -1.86 TPSA 507.8 3 viol. ✓ Clean c1cc(ccc1[C@H](CCCc2c(nc(nc2O)N)N)C(C(F)(F)F)(O…
NHE RCSB PDB Q83AY9 207.3 Da LogP 0.80 TPSA 66.4 ✓ Ro5 ✓ Clean C1CCC(CC1)NCCS(=O)(=O)O
NHR RCSB PDB P08179 482.4 Da LogP 1.38 TPSA 213.0 1 viol. ✓ Clean c1cc(ccc1[C@@H](Cc2ccc3c(c2)c(nc(n3)N)O)C(=O)O)…
NHS RCSB PDB P08179 482.4 Da LogP 0.96 TPSA 212.8 1 viol. ✓ Clean c1cc(ccc1[C@H](Cc2ccc3c(c2)C(=O)NC(=N3)N)C(=O)O…
U89 RCSB PDB P08179 715.7 Da LogP -0.31 TPSA 317.7 3 viol. ✓ Clean c1cc(ccc1C(=O)N[C@@H](CCC(=O)O)C(=O)O)N(CCCC2=C…
V97 RCSB PDB P22102 478.6 Da LogP 2.24 TPSA 175.5 ✓ Ro5 ✓ Clean c1cc(sc1CCCCc2cc3c(s2)N=C(NC3=O)N)C(=O)N[C@@H](…

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.