Protein target profile

VK055_3025

ssDNA-binding protein

Genome: KpATCC43816 Gene: ssb AIK81610.1 3D evidence: Experimental + ColabFold model UniProt A6TGW7
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Length 174
Pocket druggability 0.003
Direct ligand evidence 0 52 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.

Main supporting evidence

Experimental structure available At least one PDB experimental structure is loaded, not just a predicted model - stronger structural coverage than AlphaFold/ColabFold alone. Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Structure available Experimental + ColabFold model Ligand evidence via structure/bioactivity 2 structural and 0 bioactivity records.

Risks to review

Human similarity Top human hit identity: 38.889%. Microbiome similarity 156 of 4744 screened genomes (3.3%) have a significant similarity hit. Weak predicted binding pocket FPocket selected-pocket score 0.00.

Evidence gaps

No metabolic context No SBML/network-derived reaction evidence is loaded for 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 (%)
38.889 Lower values reduce human off-target concern.
Human E-value
3.24e-16
Gut microbiome similarity
3.3% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
93.82 Higher values support similarity to known essential genes.
DEG E-value
1.23e-118 Smaller values mean stronger essential-gene similarity.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
80.32 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

PDB experimental structure

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 0.003
Structure 7F2N
Pocket Pocket 2
P2Rank
Structure 7F2N
Pocket No pockets
ColabFold model
FPocket 0.083 · Pocket 5
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 156 / 4744 genomes with a hit
Prevalence 3.3%

Cross-references

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

Sequence

UniProt A6TGW7

Structure

PDB 4NL8 PDB 7F2N

Sequence

Primary amino-acid sequence viewer.

MASRGVNKVILVGNLGQDPEVRYMPSGGAVANFTLATSESWRDKQTGEMKEQTEWHRVVLFGKLAEVAGEYLRKGSQVYIEGQLRTRKWTDQSGQDKYTTEVVVNVGGTMQMLGGRQGGGAPAGGGQQQGGWGQPQQPQGGNQFSGGAQSRPQQQAPAAPSNEPPMDFDDDIPF

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 GO

Gene Ontology (GO)

2
  • GO:0003697 Binding to single-stranded DNA.
  • GO:0006260 The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by the origin recognition complex, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

21 records
Show feature table
Start End DB Term Name
6 111 ProSiteProfiles PS50935 Single-strand binding (SSB) domain profile.
6 111 InterPro IPR000424 Primosome PriB/single-strand DNA-binding
9 105 CDD cd04496 SSB_OBF
9 105 InterPro IPR000424 Primosome PriB/single-strand DNA-binding
129 157 MobiDBLite mobidb-lite consensus disorder prediction
2 143 Gene3D G3DSA:2.40.50.140 -
2 143 InterPro IPR012340 Nucleic acid-binding, OB-fold
6 112 Pfam PF00436 Single-strand binding protein family
6 112 InterPro IPR000424 Primosome PriB/single-strand DNA-binding
3 149 PANTHER PTHR10302 SINGLE-STRANDED DNA-BINDING PROTEIN
3 149 InterPro IPR011344 Single-stranded DNA-binding protein
2 142 FunFam G3DSA:2.40.50.140:FF:000065 Single-stranded DNA-binding protein
4 174 SUPERFAMILY SSF50249 Nucleic acid-binding proteins
4 174 InterPro IPR012340 Nucleic acid-binding, OB-fold
2 157 PIRSF PIRSF002070 SSB
2 157 InterPro IPR011344 Single-stranded DNA-binding protein
4 174 NCBIfam TIGR00621 single-stranded DNA-binding protein
4 174 InterPro IPR011344 Single-stranded DNA-binding protein
109 174 MobiDBLite mobidb-lite consensus disorder prediction
6 117 Hamap MF_00984 Single-stranded DNA-binding protein.
6 117 InterPro IPR011344 Single-stranded DNA-binding protein

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.

Download VMD script Full viewer

No pockets are loaded yet for the displayed PDB 7F2N structure. Run experimental pocket backfill to show FPocket/P2Rank overlays on this structure.

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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'.
All structural evidence 2 experimental · 1 predicted

Structural evidence

2 + 1

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
PDB 4NL8
X-ray — A —
PDBe RCSB PDBj File
Loaded
PDB 7F2N
X-ray — A —
PDBe RCSB PDBj File
Viewing
ColabFold VK055_3025
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.

52 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 2 records from similar proteins
Structural ligands 2 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
MYC PDB via homolog 318.2 Da · LogP 1.69 · TPSA 151.6 Open detail RCSB PDB
URF PDB via homolog Detail RCSB PDB
ZINC3874317 ZINC proposed compound · Tanimoto 1.000 Detail ZINC
ZINC6483599 ZINC proposed compound · Tanimoto 0.769 Detail ZINC
ZINC3869685 ZINC proposed compound · Tanimoto 0.757 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
MYC RCSB PDB
5YUN
P40947 318.2 Da LogP 1.69 TPSA 151.6 1 viol. Alert c1c(cc(c(c1O)O)O)C2=C(C(=O)c3c(cc(cc3O2)O)O)O
URF RCSB PDB
7D8J
A0A3F2YLU4 130.1 Da LogP -0.80 TPSA 65.7 ✓ Ro5 ✓ Clean C1=C(C(=O)NC(=O)N1)F

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.