KpKP13 Protein target profile

DNA polymerase III subunit delta'

Accession: KP13_04913

Gene: AHE45273.1 holB 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GVI6
Length 334
Pocket druggability (P2Rank · AlphaFold DB model) 0.426
Direct ligand evidence 0 53 total records
Functional annotation 1 EC 6 GO
Target summary

Promising target candidate with multiple supporting evidence streams.

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
No hit
Gut microbiome similarity
2.0% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
72.156 Higher values support similarity to known essential genes.
DEG E-value
1.88e-161 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
95.04 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) 0.426
Structure A0A0H3GVI6
Pocket Pocket 1
Druggability (FPocket) 0.423
Structure A0A0H3GVI6
Pocket Pocket 3
ColabFold model
P2Rank 0.305 · Pocket 1
FPocket 0.259 · Pocket 2
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 96 / 4744 genomes with a hit
Prevalence 2.0%

Sequence

Primary amino-acid sequence viewer.

MKWYPWLRPSFEQLVGSYQAGRGHHALLLQSLNGMGGEALIYALCRFLMCRQPEGHKSCGHCHSCQLMQAGTHPDYYALSPEKGKSALGIDAVRDVNEKLYEHARLGGAKVVWISDAALLTDAAANALLKTLEEPPENTWFFLACEEPARLLTTLRSRCRLHHLAPPSEPYALAWLEREVSLPQESLLTALRLCASAPAAALELLQEPLWTARQQLCQALAATLASGDWLALLPILNHEQAAVRLHWLASLLVDAQKRQQGITLVSNPDVWPLLEQLAHSLPAARLQAIAHDVCTCREQLLNVVGVNRELLLTERLLRWEHYLQPGTVLPVSHL

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Subcellular localization

Localization
Cytoplasmic

Enzyme Commission (EC)

1

Gene Ontology (GO)

6
  • GO:0009360 The DNA polymerase III holoenzyme is a complex that contains 10 different types of subunits. These subunits are organized into 3 functionally essential sub-assemblies: the pol III core, the beta sliding clamp processivity factor and the clamp-loading complex. The pol III core carries out the polymerase and the 3'-5' exonuclease proofreading activities. The polymerase is tethered to the template via the sliding clamp processivity factor. The clamp-loading complex assembles the beta processivity factor onto the primer template and plays a central role in the organization and communication at the replication fork.
  • 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.
  • GO:0003887 Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); DNA-template-directed extension of the 3'-end of a DNA strand by one nucleotide at a time.
  • GO:0008408 Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end.
  • GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
  • GO:0006261 A DNA replication process that uses parental DNA as a template for the DNA-dependent DNA polymerases that synthesize the new strands.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

15 records
Show feature table
Start End DB Term Name
1 167 FunFam G3DSA:3.40.50.300:FF:000890 DNA polymerase III subunit delta
168 207 Gene3D G3DSA:1.10.8.10 -
209 329 Gene3D G3DSA:1.20.272.10 -
12 200 NCBIfam TIGR00678 DNA polymerase III subunit delta'
12 200 InterPro IPR004622 DNA polymerase III, delta prime subunit
1 206 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
1 206 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
1 167 Gene3D G3DSA:3.40.50.300 -
1 167 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
209 321 Pfam PF09115 DNA polymerase III, delta subunit, C terminal
209 321 InterPro IPR015199 DNA polymerase III, delta subunit, C-terminal
11 166 Pfam PF13177 DNA polymerase III, delta subunit
209 328 SUPERFAMILY SSF48019 post-AAA+ oligomerization domain-like
209 328 InterPro IPR008921 DNA polymerase III, clamp loader complex, gamma/delta/delta subunit, C-terminal
18 178 PANTHER PTHR11669 REPLICATION FACTOR C / DNA POLYMERASE III GAMMA-TAU SUBUNIT

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
0.426
Likely same site as FPocket 11 2.5 Å 11 shared residues 100% of smaller site
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Surrounding area
Pocket 2 P2Rank #2
0.111
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Surrounding area
Pocket 3 P2Rank #3
0.082
Likely same site as FPocket 3 3.9 Å 7 shared residues 100% of smaller site
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Surrounding area
Pocket 4 P2Rank #4
0.018
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Surrounding area
Pocket 5 P2Rank #5
0.012
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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
0.423
Likely same site as P2Rank 3 3.9 Å 7 shared residues 100% of smaller site
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Surrounding area
Pocket 2 FPocket #11
0.27
Likely same site as P2Rank 1 2.5 Å 11 shared residues 100% of smaller site
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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_A0A0H3GVI6
AlphaFold DB full sequence Viewing
ColabFold KP13_04913
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
AGS PDB via homolog 523.2 Da · LogP -1.51 · TPSA 262.1 Open detail RCSB PDB
BEF PDB via homolog Detail RCSB PDB
ETX PDB via homolog Detail RCSB PDB
ZINC5650743 ZINC proposed compound · Tanimoto 0.875 Detail ZINC
ZINC6403917 ZINC proposed compound · Tanimoto 0.875 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
AGS RCSB PDB P06710 523.2 Da LogP -1.51 TPSA 262.1 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
BEF RCSB PDB P06710 66.0 Da LogP 0.88 TPSA 0.0 ✓ Ro5 ✓ Clean [Be-](F)(F)F
ETX RCSB PDB Q9WZM9 90.1 Da LogP 0.02 TPSA 29.5 ✓ Ro5 ✓ Clean CCOCCO

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.