Protein target profile

KP13_03812

Phosphoribosylformylglycinamidine cyclo-ligase

Genome: KpKP13 Gene: AHE43297.1 purM 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GRL0
Length 345
Pocket druggability 0.456
Direct ligand evidence 0 53 total records
Functional annotation 0 EC 2 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 (%)
49.412 Lower values reduce human off-target concern.
Human E-value
1.41e-106
Gut microbiome similarity
31.1% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
68.091 Higher values support similarity to known essential genes.
DEG E-value
3.17e-175 Smaller values mean stronger essential-gene similarity.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
96.67 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 0.456
Structure A0A0H3GRL0
Pocket Pocket 16
P2Rank 0.222
Structure A0A0H3GRL0
Pocket Pocket 1
ColabFold model
FPocket 0.644 · Pocket 2
P2Rank 0.27 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 1476 / 4744 genomes with a hit
Prevalence 31.1%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MTDKTSLSYKDAGVDIDAGNALVDRIKGVVKKTRRPEVMGGLGGFGALCALPQKYREPVLVSGTDGVGTKLRLAMDLKRHDTIGIDLVAMCVNDLVVQGAEPLFFLDYYATGKLDVDTAASVINGIAEGCLQSGCALVGGETAEMPGMYHGEDYDVAGFCVGVVEKSEIIDGSKVTDGDVLVALASSGPHSNGYSLVRKIIEVSGVEPQTTDLDGKPLADHLLAPTRIYVKSVLDLIASVDVHAIAHLTGGGFWENIPRVLPDNTQAIIDESSWQWPSVFNWLQTAGNVSQHEMYRTFNCGVGMIIALPAAEADKAIALLNDKGENAWKIGYIKASDSEQRVVIA

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 GO

Gene Ontology (GO)

2
  • GO:0004641 Catalysis of the reaction: 2-(formamido)-N(1)-(5-phospho-D-ribosyl)acetamidine + ATP = 5-amino-1-(5-phospho-D-ribosyl)imidazole + ADP + 2 H+ + 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.

22 records
Show feature table
Start End DB Term Name
171 345 Gene3D G3DSA:3.90.650.10 -
171 345 InterPro IPR036676 PurM-like, C-terminal domain superfamily
7 335 NCBIfam TIGR00878 phosphoribosylformylglycinamidine cyclo-ligase
7 335 InterPro IPR004733 Phosphoribosylformylglycinamidine cyclo-ligase
7 170 SUPERFAMILY SSF55326 PurM N-terminal domain-like
7 170 InterPro IPR036921 PurM-like, N-terminal domain superfamily
171 345 FunFam G3DSA:3.90.650.10:FF:000001 Phosphoribosylformylglycinamidine cyclo-ligase
4 343 PANTHER PTHR10520 TRIFUNCTIONAL PURINE BIOSYNTHETIC PROTEIN ADENOSINE-3-RELATED
4 343 InterPro IPR004733 Phosphoribosylformylglycinamidine cyclo-ligase
177 342 Pfam PF02769 AIR synthase related protein, C-terminal domain
177 342 InterPro IPR010918 PurM-like, C-terminal domain
61 164 Pfam PF00586 AIR synthase related protein, N-terminal domain
61 164 InterPro IPR016188 PurM-like, N-terminal domain
40 334 CDD cd02196 PurM
40 334 InterPro IPR004733 Phosphoribosylformylglycinamidine cyclo-ligase
6 170 FunFam G3DSA:3.30.1330.10:FF:000001 Phosphoribosylformylglycinamidine cyclo-ligase
171 342 SUPERFAMILY SSF56042 PurM C-terminal domain-like
171 342 InterPro IPR036676 PurM-like, C-terminal domain superfamily
7 344 Hamap MF_00741 Phosphoribosylformylglycinamidine cyclo-ligase [purM].
7 344 InterPro IPR004733 Phosphoribosylformylglycinamidine cyclo-ligase
6 170 Gene3D G3DSA:3.30.1330.10 -
6 170 InterPro IPR036921 PurM-like, N-terminal domain superfamily

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 #16
0.456
Likely same site as P2Rank 1 3.0 Å 12 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
0.222
Likely same site as FPocket 16 3.0 Å 12 shared residues 100% of smaller site
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.006
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.005
Show in viewer
Surrounding area
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_A0A0H3GRL0
AlphaFold DB full sequence Viewing
ColabFold KP13_03812
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.

53 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 3 records from similar proteins
Structural ligands 3 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
ANP PDB via homolog 506.2 Da · LogP -2.06 · TPSA 281.9 Open detail RCSB PDB
CAC PDB via homolog Detail RCSB PDB
POP PDB via homolog Detail RCSB PDB
ZINC12501520 ZINC proposed compound · Tanimoto 1.000 Detail ZINC
ZINC3874716 ZINC proposed compound · Tanimoto 1.000 Detail ZINC

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
ANP RCSB PDB Q5F973 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)…
CAC RCSB PDB A6LDR8 137.0 Da LogP -0.52 TPSA 40.1 ✓ Ro5 ✓ Clean C[As](=O)(C)[O-]
POP RCSB PDB Q5NGF2 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.