Protein target profile

VK055_5117

2,3-dihydroxybenzoate-AMP ligase

Genome: KpATCC43816 Gene: AIK83643.1 ybtE 3D evidence: AlphaFold DB model + ColabFold model Metabolism 1 reaction UniProt A0A0H3GSA9
Length 525
Pocket druggability 0.932
Metabolic reactions 1
Chokepoint No
Direct ligand evidence 0 139 total records
Functional annotation 0 EC 1 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 (%)
36.076 Lower values reduce human off-target concern.
Human E-value
1.3e-17
Gut microbiome similarity
0.3% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
45.328 Higher values support similarity to known essential genes.
DEG E-value
1.86e-133 Smaller values mean stronger essential-gene similarity.

Localization

Localization
CytoplasmicMembrane

Structure confidence

ColabFold pLDDT
92.16 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 0.932
Structure A0A0H3GSA9
Pocket Pocket 1
P2Rank 0.983
Structure A0A0H3GSA9
Pocket Pocket 1
ColabFold model
FPocket 0.807 · Pocket 1
P2Rank 0.964 · Pocket 1
Core conservation Accessory gene
Roary accessory
CoreCruncher accessory
Gut microbiome 14 / 4744 genomes with a hit
Prevalence 0.3%

Cross-references

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

Chemistry

ChEMBL CHEMBL608841 ChEMBL CHEMBL611772 ChEMBL CHEMBL611766 ChEMBL CHEMBL611777 ChEMBL CHEMBL612049 ChEMBL CHEMBL612048 ChEMBL CHEMBL611785 ChEMBL CHEMBL609105 ChEMBL CHEMBL612052 ChEMBL CHEMBL608839 ChEMBL CHEMBL611782 ChEMBL CHEMBL611784 ChEMBL CHEMBL611775 ChEMBL CHEMBL609101 ChEMBL CHEMBL611780 ChEMBL CHEMBL612041 ChEMBL CHEMBL611774 ChEMBL CHEMBL5430701 ChEMBL CHEMBL611771 ChEMBL CHEMBL608842 ChEMBL CHEMBL611767 ChEMBL CHEMBL611783 ChEMBL CHEMBL456074 ChEMBL CHEMBL371502 ChEMBL CHEMBL612040 ChEMBL CHEMBL612037 ChEMBL CHEMBL1627105 ChEMBL CHEMBL608843 ChEMBL CHEMBL609100 ChEMBL CHEMBL612057 ChEMBL CHEMBL518346 ChEMBL CHEMBL608840 ChEMBL CHEMBL612053 ChEMBL CHEMBL612051 ChEMBL CHEMBL218023 ChEMBL CHEMBL609107 ChEMBL CHEMBL612044 ChEMBL CHEMBL611789 ChEMBL CHEMBL608838 ChEMBL CHEMBL609103 ChEMBL CHEMBL609108 ChEMBL CHEMBL611786 ChEMBL CHEMBL387162 ChEMBL CHEMBL611776 ChEMBL CHEMBL612022 ChEMBL CHEMBL612056 ChEMBL CHEMBL218683 ChEMBL CHEMBL609097 ChEMBL CHEMBL516501 ChEMBL CHEMBL608844 ChEMBL CHEMBL612042 ChEMBL CHEMBL612046 ChEMBL CHEMBL220160 ChEMBL CHEMBL461568 ChEMBL CHEMBL1162040 ChEMBL CHEMBL4299745 ChEMBL CHEMBL1162033 ChEMBL CHEMBL1162035 ChEMBL CHEMBL1162037 ChEMBL CHEMBL4299747 ChEMBL CHEMBL4299749 ChEMBL CHEMBL1162034 ChEMBL CHEMBL1162036 ChEMBL CHEMBL4299748 ChEMBL CHEMBL608845 ChEMBL CHEMBL1162030 ChEMBL CHEMBL1162039 ChEMBL CHEMBL447500 ChEMBL CHEMBL1162032 ChEMBL CHEMBL385125 ChEMBL CHEMBL611788 ChEMBL CHEMBL438072 ChEMBL CHEMBL4168282 ChEMBL CHEMBL459679 ChEMBL CHEMBL1162041 ChEMBL CHEMBL1162045 ChEMBL CHEMBL611769 ChEMBL CHEMBL612058 ChEMBL CHEMBL437891 ChEMBL CHEMBL609098 ChEMBL CHEMBL611787 ChEMBL CHEMBL384655

Metabolic context

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

Explore metabolic network
Relative network centrality 0.0% more central than 0.0% of genes in this genome
Chokepoint Not a chokepoint
Pathways

No specific KEGG pathway assigned - this reaction either has no KEGG mapping, or only matches a generic overview map with no route-level information.

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.

MNSSFESLIEQYPLPIAEQLRHWAARYASRIAVVDAKGSLTYSALDAQVDELAAGLSSLGLCSGEHVIVQLPNDNAFVTLLFALLRLGVIPVLAMPSQRALDIDALIELAQPVAYVIHGENHAELARQMAHKHACLRHVLVAGETVSDDFTPLFSLHGERQAWPQPDVSATALLLLSGGTTGTPKLIPRRHADYSYNFSASAELCGISQQSVYLAVLPVAHNFPLACPGILGTLACGGKVVLTDSASCDEVMPLIAQERVTHVALVPALAQLWVQAREWEDSDLSSLRVIQAGGARLDPTLAEQVIATFDCTLQQVFGMAEGLLCFTRLDDPHATILHSQGRPLSPLDEIRIVDQDENDVAPGETGQLLTRGPYTISGYYRAPAHNAQAFTAQGFYRTGDNVRLDEVGNLHVEGRIKEQINRAGEKIAAAEVESALLRLAEVQDCAVVAAPDTLLGERICAFIIAQQVPTDYQQLRQQLTRMGLSAWKIPDQIEFLDHWPLTAVGKIDKKRLTALAVDRYRHSAQ

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 GO

Gene Ontology (GO)

1
  • GO:0016878 Catalysis of the joining of an acid and a thiol via a carbon-sulfur bond, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

18 records
Show feature table
Start End DB Term Name
13 166 FunFam G3DSA:3.40.50.980:FF:000004 2,3-dihydroxybenzoate-AMP ligase
341 415 FunFam G3DSA:2.30.38.10:FF:000003 Vibriobactin-specific 2,3-dihydroxybenzoate-AMP ligase
431 506 Pfam PF13193 AMP-binding enzyme C-terminal domain
431 506 InterPro IPR025110 AMP-binding enzyme, C-terminal domain
417 520 FunFam G3DSA:3.30.300.30:FF:000008 2,3-dihydroxybenzoate-AMP ligase
168 340 FunFam G3DSA:3.40.50.980:FF:000003 Vibriobactin-specific 2,3-dihydroxybenzoate-AMP ligase
4 512 CDD cd05920 23DHB-AMP_lg
15 166 Gene3D G3DSA:3.40.50.980 -
341 415 Gene3D G3DSA:2.30.38.10 Luciferase; Domain 3
169 340 Gene3D G3DSA:3.40.50.980 -
417 522 Gene3D G3DSA:3.30.300.30 -
417 522 InterPro IPR045851 AMP-binding enzyme, C-terminal domain superfamily
174 185 ProSitePatterns PS00455 Putative AMP-binding domain signature.
174 185 InterPro IPR020845 AMP-binding, conserved site
21 422 Pfam PF00501 AMP-binding enzyme
21 422 InterPro IPR000873 AMP-dependent synthetase/ligase domain
10 518 SUPERFAMILY SSF56801 Acetyl-CoA synthetase-like
10 517 PANTHER PTHR43767 LONG-CHAIN-FATTY-ACID--COA LIGASE

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 #1
0.932
Likely same site as P2Rank 1 1.6 Å 48 shared residues 94% 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
0.983
Likely same site as FPocket 1 1.6 Å 48 shared residues 94% of smaller site
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.11
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.11
Show in viewer
Surrounding area
Site 4 P2Rank #4
0.054
Show in viewer
Surrounding area
Site 5 P2Rank #5
0.01
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_A0A0H3GSA9
AlphaFold DB full sequence Viewing
ColabFold VK055_5117
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.

139 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 89 records from similar proteins
Structural ligands 7 0 loaded crystals
Measured bioactivity 82 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
B5M PDB via homolog 481.4 Da · LogP 0.02 · TPSA 212.4 Open detail RCSB PDB
B5V PDB via homolog Detail RCSB PDB
B5Y PDB via homolog Detail RCSB PDB
DBH PDB via homolog Detail RCSB PDB
J2J 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
B5M RCSB PDB A0A140DJY3 481.4 Da LogP 0.02 TPSA 212.4 1 viol. ✓ Clean Cc1cccc(c1C(=O)OP(=O)(O)OC[C@H]2[C@H]([C@H]([C@…
B5V RCSB PDB A0A140DJY3 467.3 Da LogP -0.29 TPSA 212.4 1 viol. ✓ Clean c1ccc(c(c1)C(=O)OP(=O)(O)OC[C@H]2[C@H]([C@H]([C…
B5Y RCSB PDB A0A140DJY3 481.4 Da LogP 0.02 TPSA 212.4 1 viol. ✓ Clean Cc1ccc(c(c1)C(=O)OP(=O)(O)OC[C@H]2[C@H]([C@H]([…
DBH RCSB PDB P40871 154.1 Da LogP 0.80 TPSA 77.8 ✓ Ro5 Alert c1cc(c(c(c1)O)O)C(=O)O
J2J RCSB PDB Q47NR5 483.3 Da LogP -0.59 TPSA 232.6 2 viol. Alert c1cc(c(c(c1)O)O)C(=O)OP(=O)(O)OC[C@@H]2[C@H]([C…
OOB RCSB PDB A0A140DJY3 451.3 Da LogP 0.00 TPSA 192.1 1 viol. ✓ Clean c1ccc(cc1)C(=O)OP(=O)(O)OC[C@@H]2[C@H]([C@H]([C…
SAL RCSB PDB A0A140DJY3 138.1 Da LogP 1.09 TPSA 57.5 ✓ Ro5 ✓ Clean c1ccc(c(c1)C(=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.