KpKP13 Protein target profile

Amidophosphoribosyltransferase

Accession: KP13_01020

Gene: purF AHE43452.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3H133
Length 505
Pocket druggability (P2Rank · AlphaFold DB model) 0.643
Direct ligand evidence 0 63 total records
Functional annotation 1 EC 4 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 (%)
40.323 Lower values reduce human off-target concern.
Human E-value
5.36e-20
Gut microbiome similarity
5.8% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
64.213 Higher values support similarity to known essential genes.
DEG E-value
0.0 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
92.25 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) 0.643
Structure A0A0H3H133
Pocket Pocket 1
Druggability (FPocket) 0.392
Structure A0A0H3H133
Pocket Pocket 31
ColabFold model
P2Rank 0.676 · Pocket 1
FPocket 0.517 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 273 / 4744 genomes with a hit
Prevalence 5.8%

Sequence

Primary amino-acid sequence viewer.

MCGIVGIAGVMPVNQSIYDALTVLQHRGQDAAGIITIDANNCFRLRKANGLVSDVFEARHMQRMQGNMGIGHVRYPTAGSSSASEAQPFYVNSPYGITLAHNGNLTNAHELRKKLFEEKRRHINTTSDSEILLNIFASELDNFRHYPLEADNIFAAIAATNRLIRGAYACVAMIIGHGMVAFRDPNGIRPLVLGKRDVGDGRTEYMVASESVALDTLGFEFLRDVAPGEAVYITEKGQLYTRQCADNPVSNPCLFEYVYFARPDSFIDKISVYSARVNMGTKLGEKIAREWEDLDIDVVIPIPETSCDIALEIARILDKPYRQGFVKNRYVGRTFIMPGQQLRRKSVRRKLNANRAEFRDKNVLLVDDSIVRGTTSEQIIEMAREAGAKKVYLASAAPEIRFPNVYGIDMPTANELIAHGREVDEIRQIIGADGLIFQDLNDLIDAVRAENPDIQQFECSVFNGVYVTRDVDQQYLDYLDSLRNDDAKAVQLQNEVENLEMHNEG

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Subcellular localization

Localization
Cytoplasmic

Enzyme Commission (EC)

1

Gene Ontology (GO)

4
  • GO:0009113 The chemical reactions and pathways resulting in the formation of purine nucleobases, one of the two classes of nitrogen-containing ring compounds found in DNA and RNA, which include adenine and guanine.
  • GO:0004044 Catalysis of the reaction: 5-phospho-beta-D-ribosylamine + L-glutamate + diphosphate = 5-phospho-alpha-D-ribose 1-diphosphate + L-glutamine + H2O.
  • GO:0000287 Binding to a magnesium (Mg) ion.
  • 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.

26 records
Show feature table
Start End DB Term Name
2 268 CDD cd00715 GPATase_N
2 268 InterPro IPR035584 Amidophosphoribosyltransferase, N-terminal
283 398 CDD cd06223 PRTases_typeI
283 398 InterPro IPR000836 Phosphoribosyltransferase domain
1 483 PIRSF PIRSF000485 Pur1
1 483 InterPro IPR005854 Amidophosphoribosyltransferase
1 478 PANTHER PTHR11907 AMIDOPHOSPHORIBOSYLTRANSFERASE
482 502 Coils Coil Coil
281 443 Gene3D G3DSA:3.40.50.2020 -
281 443 InterPro IPR029057 Phosphoribosyltransferase-like
2 290 FunFam G3DSA:3.60.20.10:FF:000011 Amidophosphoribosyltransferase
65 196 Pfam PF13522 Glutamine amidotransferase domain
2 236 ProSiteProfiles PS51278 Glutamine amidotransferase type 2 domain profile.
2 236 InterPro IPR017932 Glutamine amidotransferase type 2 domain
2 416 Gene3D G3DSA:3.60.20.10 Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
2 416 InterPro IPR029055 Nucleophile aminohydrolases, N-terminal
2 466 NCBIfam TIGR01134 amidophosphoribosyltransferase
2 466 InterPro IPR005854 Amidophosphoribosyltransferase
2 259 SUPERFAMILY SSF56235 N-terminal nucleophile aminohydrolases (Ntn hydrolases)
2 259 InterPro IPR029055 Nucleophile aminohydrolases, N-terminal
1 466 Hamap MF_01931 Amidophosphoribosyltransferase [purF].
1 466 InterPro IPR005854 Amidophosphoribosyltransferase
252 485 SUPERFAMILY SSF53271 PRTase-like
252 485 InterPro IPR029057 Phosphoribosyltransferase-like
287 394 Pfam PF00156 Phosphoribosyl transferase domain
287 394 InterPro IPR000836 Phosphoribosyltransferase domain

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
0.643
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Surrounding area
Pocket 2 P2Rank #2
0.407
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Surrounding area
Pocket 3 P2Rank #3
0.024
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Surrounding area
Pocket 4 P2Rank #4
0.008
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Surrounding area
Pocket 5 P2Rank #5
0.004
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Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #31
0.392
Show in viewer
Surrounding area
Residue sets
UniProt: Active site:2-2 Nucleophile
UniProt: Binding site:305-305
UniProt: Binding site:367-367
UniProt: Binding site:368-368
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_A0A0H3H133
AlphaFold DB full sequence Viewing
ColabFold KP13_01020
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.

63 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 13 records from similar proteins
Structural ligands 10 0 loaded crystals
Measured bioactivity 3 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
5GP PDB via homolog 363.2 Da · LogP -2.57 · TPSA 206.0 Open detail RCSB PDB
AGP PDB via homolog Detail RCSB PDB
F6R PDB via homolog Detail RCSB PDB
G4P PDB via homolog Detail RCSB PDB
G6Q 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
5GP RCSB PDB P0AG16 363.2 Da LogP -2.57 TPSA 206.0 1 viol. ✓ Clean c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O…
AGP RCSB PDB P17169 261.2 Da LogP -3.50 TPSA 173.7 1 viol. ✓ Clean C([C@@H]([C@H]([C@@H]([C@@H](COP(=O)(O)O)O)O)O)…
F6R RCSB PDB P17169 260.1 Da LogP -3.26 TPSA 164.8 1 viol. ✓ Clean C([C@H]([C@H]([C@@H](C(=O)CO)O)O)O)OP(=O)(O)O
G4P RCSB PDB P0AG16 603.2 Da LogP -2.22 TPSA 345.6 3 viol. ✓ Clean c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O…
G6Q RCSB PDB P17169 260.1 Da LogP -3.26 TPSA 164.8 1 viol. ✓ Clean C([C@H]([C@H]([C@@H]([C@H](C=O)O)O)O)O)OP(=O)(O…
HGA RCSB PDB P17169 162.1 Da LogP -1.32 TPSA 112.7 ✓ Ro5 ✓ Clean C(CC(=O)NO)[C@@H](C(=O)O)N
N7Y RCSB PDB P0AG16 587.2 Da LogP -1.51 TPSA 325.7 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
ONL RCSB PDB P0AG16 145.2 Da LogP -0.23 TPSA 80.4 ✓ Ro5 ✓ Clean CC(=O)CC[C@@H](C(=O)O)N
PCP RCSB PDB P0AG16 388.1 Da LogP -1.57 TPSA 220.5 1 viol. ✓ Clean C1[C@@H]([C@H]([C@H]([C@H]1O[P@](=O)(O)OP(=O)(O…
PIN RCSB PDB P0AG16 302.4 Da LogP -1.62 TPSA 115.2 ✓ Ro5 ✓ Clean C1CN(CCN1CCS(=O)(=O)O)CCS(=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.