KpKP13 Protein target profile

Adenylosuccinate lyase

Accession: KP13_04866

Gene: AHE45226.1 purB 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GVM8
Length 456
Pocket druggability (P2Rank · AlphaFold DB model) 0.116
Direct ligand evidence 0 57 total records
Functional annotation 1 EC 8 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 (%)
23.247 Lower values reduce human off-target concern.
Human E-value
5.01e-07
Gut microbiome similarity
12.6% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Structure confidence

ColabFold pLDDT
97.82 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) 0.116
Structure A0A0H3GVM8
Pocket Pocket 1
Druggability (FPocket) 0.248
Structure A0A0H3GVM8
Pocket Pocket 3
ColabFold model
P2Rank 0.071 · Pocket 1
FPocket 0.145 · Pocket 7
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 598 / 4744 genomes with a hit
Prevalence 12.6%

Sequence

Primary amino-acid sequence viewer.

MELSSLTAVSPVDGRYGDKVSALRGIFSEFGLLKFRVQVEVRWLQKLAAHAAIKEVPAFAADANGFLDKIVADFSVEDAERIKTIERTTNHDVKAVEYFLKEKVADVAELHAVSEFIHFACTSEDINNLSHALMLKTARDEVVLPYWRKLIDAVKDLATQYRDVPLLSRTHGQPATPSTMGKEMANVAYRMERQYRQLNQVEILGKINGAVGNYNAHIAAYPEVDWHQFSEEFVTSLGIQWNPYTTQIEPHDYIAELFDCIARFNTILIDFDRDVWGYIALNHFKQKTIAGEIGSSTMPHKVNPIDFENSEGNLGLANAVMQHLASKLPVSRWQRDLTDSTVLRNLGVGIGYALIAYQSTLKGISKLELNQDRLLDELDHNWEVLAEPIQTVMRRYGIEKPYEKLKELTRGKRVDAEGMKQFIDSLALPEEEKVRLKAMTPANYIGRATTMVDELK

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 8 GO

Subcellular localization

Localization
Cytoplasmic

Enzyme Commission (EC)

1

Gene Ontology (GO)

8
  • 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:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
  • GO:0004018 Catalysis of the reaction: N6-(1,2-dicarboxyethyl)AMP = fumarate + AMP.
  • GO:0006188 The chemical reactions and pathways resulting in the formation of IMP, inosine monophosphate.
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0070626 Catalysis of the reaction: (S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido)succinate = fumarate + 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide.
  • GO:0044208 The chemical reactions and pathways resulting in the formation of adenosine monophosphate (AMP) from inosine 5'-monophosphate (IMP).
  • 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.

28 records
Show feature table
Start End DB Term Name
12 455 NCBIfam TIGR00928 adenylosuccinate lyase
12 455 InterPro IPR004769 Adenylosuccinate lyase
23 446 CDD cd01598 PurB
294 303 ProSitePatterns PS00163 Fumarate lyases signature.
294 303 InterPro IPR020557 Fumarate lyase, conserved site
14 312 Pfam PF00206 Lyase
14 312 InterPro IPR022761 Fumarate lyase, N-terminal
382 445 Gene3D G3DSA:1.10.40.30 -
118 384 FunFam G3DSA:1.20.200.10:FF:000004 Adenylosuccinate lyase
118 449 Gene3D G3DSA:1.20.200.10 Fumarase/aspartase (Central domain)
382 445 FunFam G3DSA:1.10.40.30:FF:000004 Adenylosuccinate lyase
10 454 SUPERFAMILY SSF48557 L-aspartase-like
10 454 InterPro IPR008948 L-Aspartase-like
163 181 PRINTS PR00149 Fumarate lyase superfamily signature
163 181 InterPro IPR000362 Fumarate lyase family
294 310 PRINTS PR00149 Fumarate lyase superfamily signature
294 310 InterPro IPR000362 Fumarate lyase family
117 135 PRINTS PR00149 Fumarate lyase superfamily signature
117 135 InterPro IPR000362 Fumarate lyase family
251 278 PRINTS PR00149 Fumarate lyase superfamily signature
251 278 InterPro IPR000362 Fumarate lyase family
1 117 Gene3D G3DSA:1.10.275.10 -
1 117 InterPro IPR024083 Fumarase/histidase, N-terminal
331 445 Pfam PF08328 Adenylosuccinate lyase C-terminal
331 445 InterPro IPR013539 Adenylosuccinate lyase PurB, C-terminal
1 117 FunFam G3DSA:1.10.275.10:FF:000003 Adenylosuccinate lyase
2 454 PANTHER PTHR43411 ADENYLOSUCCINATE LYASE
2 454 InterPro IPR047136 Adenylosuccinate lyase PurB, bacteria

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
0.116
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Surrounding area
Pocket 2 P2Rank #2
0.04
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Surrounding area
Pocket 3 P2Rank #3
0.035
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Surrounding area
Pocket 4 P2Rank #4
0.019
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Surrounding area
Pocket 5 P2Rank #5
0.015
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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 #3
0.248
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_A0A0H3GVM8
AlphaFold DB full sequence Viewing
ColabFold KP13_04866
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.

57 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 7 records from similar proteins
Structural ligands 7 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
2SA PDB via homolog 463.3 Da · LogP -2.11 · TPSA 246.7 Open detail RCSB PDB
DTT PDB via homolog Detail RCSB PDB
FUM PDB via homolog Detail RCSB PDB
MLI PDB via homolog Detail RCSB PDB
N2P 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
2SA RCSB PDB P0AB89 463.3 Da LogP -2.11 TPSA 246.7 2 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
DTT RCSB PDB Q88N37 154.3 Da LogP -0.43 TPSA 40.5 ✓ Ro5 ✓ Clean C([C@@H]([C@H](CS)O)O)S
FUM RCSB PDB P0AB89 116.1 Da LogP -0.29 TPSA 74.6 ✓ Ro5 ✓ Clean C(=C/C(=O)O)\C(=O)O
MLI RCSB PDB A0A6L8PR48 102.0 Da LogP -3.12 TPSA 80.3 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(=O)[O-]
N2P RCSB PDB Q8ZPZ6 102.2 Da LogP 0.07 TPSA 52.0 ✓ Ro5 ✓ Clean C(CCN)CCN
OXL RCSB PDB Q7A0G9 88.0 Da LogP -3.51 TPSA 80.3 ✓ Ro5 ✓ Clean C(=O)(C(=O)[O-])[O-]
SIN RCSB PDB Q5NIQ1 118.1 Da LogP -0.06 TPSA 74.6 ✓ Ro5 ✓ Clean C(CC(=O)O)C(=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.