Protein target profile

VK055_2887

adenylosuccinate synthase

Genome: KpATCC43816 Gene: purA AIK81476.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism 1 reaction UniProt A0A0H3GLD4
Length 432
Pocket druggability 0.975
Metabolic reactions 1
Chokepoint Yes
Direct ligand evidence 0 65 total records
Functional annotation 1 EC 8 GO
Target summary

Strong target candidate with converging metabolic, structural and chemical evidence.

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 (%)
43.478 Lower values reduce human off-target concern.
Human E-value
6.13e-09
Gut microbiome similarity
6.9% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
96.73 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 0.975
Structure A0A0H3GLD4
Pocket Pocket 4
P2Rank 0.947
Structure A0A0H3GLD4
Pocket Pocket 1
ColabFold model
FPocket 0.996 · Pocket 1
P2Rank 0.931 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 325 / 4744 genomes with a hit
Prevalence 6.9%

Cross-references

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

Metabolic context

Reactions catalyzed, pathway membership, and centrality in the genome-scale metabolic network.

Explore metabolic network

Attractive metabolic target: catalyzes a producing chokepoint reaction in Alanine, aspartate and glutamate metabolism, no isoenzyme backup detected, more central than 99.9% of genes in this genome.

Relative network centrality 99.9% more central than 99.9% of genes in this genome
Chokepoint Chokepoint gene
Catalyzed reaction

1 reaction mapped to this gene in the metabolic model. Open the full network to see each one, with substrates/products and the reaction-reaction map.

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MGNNVVVLGTQWGDEGKGKIVDLLTERAKYVVRYQGGHNAGHTLVINGEKTVLHLIPSGILRENVTSIIGNGVVLSPAALMKEMKGLEDRGIPVRERLLLSEACPLILDYHVALDVAREKARGAKAIGTTGRGIGPAYEDKVARRGLRVGDLFDKATFADKLKEVMEYHNFQLVNFYKAEAVDYQKVLDDVMAIADILTSMVVDVSDLLDQARQRGDFVMFEGAQGTLLDIDHGTYPYVTSSNTTAGGVATGSGLGPRYVDYVLGIIKAYSTRVGAGPFPTELFDETGEFLCKQGNEFGATTGRRRRTGWLDAVAVRRAVQINSLSGFCLTKLDVLDGLKEVKICVGYRMPDGREVTTTPLAADNWEGIEPIYETMPGWSETTFGVKERSGLPQAALNYIQRIEELTGVPVDIISTGPDRTETMILRDPFDA

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 8 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

8
  • GO:0005525 Binding to GTP, guanosine triphosphate.
  • GO:0000166 Binding to a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
  • GO:0006164 The chemical reactions and pathways resulting in the formation of a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
  • GO:0004019 Catalysis of the reaction: L-aspartate + GTP + IMP = N(6)-(1,2-dicarboxyethyl)-AMP + GDP + 3 H+ + phosphate.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0000287 Binding to a magnesium (Mg) ion.
  • GO:0044208 The chemical reactions and pathways resulting in the formation of adenosine monophosphate (AMP) from inosine 5'-monophosphate (IMP).
  • GO:0046040 The chemical reactions and pathways involving IMP, inosine monophosphate.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

26 records
Show feature table
Start End DB Term Name
4 425 SMART SM00788 adenylsucc_synt
4 425 InterPro IPR001114 Adenylosuccinate synthetase
6 430 NCBIfam TIGR00184 adenylosuccinate synthase
6 430 InterPro IPR001114 Adenylosuccinate synthetase
6 424 Pfam PF00709 Adenylosuccinate synthetase
6 424 InterPro IPR001114 Adenylosuccinate synthetase
102 201 Gene3D G3DSA:1.10.300.10 Adenylosuccinate Synthetase, subunit A, domain 2
102 201 InterPro IPR042110 Adenylosuccinate synthetase, domain 2
102 201 FunFam G3DSA:1.10.300.10:FF:000001 Adenylosuccinate synthetase
6 259 Gene3D G3DSA:3.40.440.10 Adenylosuccinate Synthetase, subunit A, domain 1
6 259 InterPro IPR042109 Adenylosuccinate synthetase, domain 1
267 432 Gene3D G3DSA:3.90.170.10 Adenylosuccinate Synthetase, subunit A, domain 3
267 432 InterPro IPR042111 Adenylosuccinate synthetase, domain 3
3 431 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
3 431 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
4 424 PANTHER PTHR11846 ADENYLOSUCCINATE SYNTHETASE
4 424 InterPro IPR001114 Adenylosuccinate synthetase
1 432 Hamap MF_00011 Adenylosuccinate synthetase [purA].
1 432 InterPro IPR001114 Adenylosuccinate synthetase
11 18 ProSitePatterns PS01266 Adenylosuccinate synthetase GTP-binding site.
11 18 InterPro IPR018220 Adenylosuccinate synthase, GTP-binding site
3 425 CDD cd03108 AdSS
3 425 InterPro IPR001114 Adenylosuccinate synthetase
133 144 ProSitePatterns PS00513 Adenylosuccinate synthetase active site.
133 144 InterPro IPR033128 Adenylosuccinate synthase, active site
267 429 FunFam G3DSA:3.90.170.10:FF:000001 Adenylosuccinate synthetase

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 #4
0.975
Likely same site as P2Rank 1 1.6 Å 45 shared residues 90% 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
0.947
Likely same site as FPocket 4 1.6 Å 45 shared residues 90% of smaller site
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.056
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.049
Show in viewer
Surrounding area
Site 4 P2Rank #4
0.033
Show in viewer
Surrounding area
Residue sets
UniProt: Active site:14-14 Proton acceptor
UniProt: Active site:141-141
UniProt: Active site:42-42 Proton donor
UniProt: Binding site:13-19
UniProt: Binding site:130-130 in other chain
UniProt: Binding site:14-14
UniProt: Binding site:14-17 in other chain
UniProt: Binding site:144-144
UniProt: Binding site:225-225 in other chain
UniProt: Binding site:240-240 in other chain
UniProt: Binding site:300-306
UniProt: Binding site:304-304 in other chain
UniProt: Binding site:306-306
UniProt: Binding site:332-334
UniProt: Binding site:39-42 in other chain
UniProt: Binding site:41-41
UniProt: Binding site:41-43
UniProt: Binding site:415-417
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_A0A0H3GLD4
AlphaFold DB full sequence Viewing
ColabFold VK055_2887
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.

65 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 15 records from similar proteins
Structural ligands 15 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
DOI PDB via homolog 412.2 Da · LogP -0.94 · TPSA 206.6 Open detail RCSB PDB
DPO PDB via homolog Detail RCSB PDB
GCP PDB via homolog Detail RCSB PDB
GNH PDB via homolog Detail RCSB PDB
GNP 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
DOI RCSB PDB P0A7D4 412.2 Da LogP -0.94 TPSA 206.6 ✓ Ro5 ✓ Clean c1nc2c(c(n1)OP(=O)(O)O)ncn2[C@H]3C[C@@H]([C@H](…
DPO RCSB PDB P0A7D4 173.9 Da LogP -3.34 TPSA 135.6 ✓ Ro5 ✓ Clean [O-]P(=O)([O-])OP(=O)([O-])[O-]
GCP RCSB PDB P0A7D4 521.2 Da LogP -2.22 TPSA 289.9 3 viol. ✓ Clean c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O…
GNH RCSB PDB P0A7D4 442.2 Da LogP -2.49 TPSA 258.4 2 viol. ✓ Clean c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O…
GNP RCSB PDB P0A7D4 522.2 Da LogP -2.76 TPSA 301.9 3 viol. ✓ Clean c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O…
GPX RCSB PDB P0A7D4 505.2 Da LogP -1.29 TPSA 267.9 3 viol. ✓ Clean c1nc2c(n1[C@H]3[C@H]4[C@@H]([C@H](O3)CO[P@](=O)…
H5P RCSB PDB P0A7D4 298.1 Da LogP -3.25 TPSA 174.6 1 viol. ✓ Clean C([C@@H]1[C@H]([C@H]([C@]2(O1)C(=O)NC(=O)N2)O)O…
HDA RCSB PDB P0A7D4 119.1 Da LogP -1.08 TPSA 77.8 ✓ Ro5 ✓ Clean C(C(=O)O)N(C=O)O
IMO RCSB PDB P0A7D4 428.2 Da LogP -1.97 TPSA 226.8 2 viol. ✓ Clean c1nc2c(c(n1)OP(=O)(O)O)ncn2[C@H]3[C@@H]([C@@H](…
IMP RCSB PDB P0A7D4 348.2 Da LogP -2.15 TPSA 180.0 ✓ Ro5 ✓ Clean c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O…
MLI RCSB PDB Q81JI9 102.0 Da LogP -3.12 TPSA 80.3 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(=O)[O-]
PG6 RCSB PDB Q8ZIV7 266.3 Da LogP 0.35 TPSA 55.4 ✓ Ro5 ✓ Clean COCCOCCOCCOCCOCCOC
PGS RCSB PDB P0A7D4 445.3 Da LogP -1.84 TPSA 218.8 1 viol. ✓ Clean c1[nH+]c(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H]…
RPD RCSB PDB P0A7D4 459.3 Da LogP -3.66 TPSA 246.9 2 viol. ✓ Clean C(C[C@H](C(=O)O)[N@](CO)O)CN1C(=O)[C@@]2([C@@H]…
RPL RCSB PDB P0A7D4 459.3 Da LogP -3.66 TPSA 246.9 2 viol. ✓ Clean C(C[C@@H](C(=O)O)[N@](CO)O)CN1C(=O)[C@@]2([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.