Protein target profile

HT085_RS00010

DNA polymerase III subunit beta

Genome: NZ_AP023069.1 Gene: WHOF_00421 E8M63_03545 WHOF_00002 ESCNG_30049 TUM19854C_00020 dnaN N776_09345 3D evidence: AlphaFold DB model UniProt A0AA44U8X9 UniProt A0A1D3GQN8
Length 367
Direct ligand evidence 0 74 total records
Functional annotation 0 EC 6 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
No hit
Gut microbiome off-target
Hit

Essentiality

Essential (DEG)
Y

Localization

Localization
Cytoplasmic

Binding-site evidence

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 High
Structure
Pocket

Sequence

Primary amino-acid sequence viewer.

MLILQAERDSLLKPLQAVTGIVERRHTLPILSNVLIEGRGGQTKLLATDLEIQIDTAGPEGGAGDFRITTNAKKFQDILRALPAGALVSLDWDDNRLTLKAGKSRFALQTLPAADFPMMNVGEDISATFSLGQERFKTMLSQVQYSMAVQDIRYYLNGLLMQVEGSQLRLVATDGHRLAYAACAIDADLPRAEVILPRKTVLELFKLLNNPDDPIQIELLDKQVRFQCNGTTIVSKVIDGKFPDFNRVIPLDNDKIFVLSRAELLGALERVSILANEKFRGARLFLQPGLLSVVCSNNEQEEAREEIEIAYQGGELEVGFNIGYLMDVLRNIHSDDMQLAFGDANRSTLFTVPNNPNFKYIVMPMRI

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

6 GO

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: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:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0006271 The process in which an existing DNA strand is extended by activities including the addition of nucleotides to the 3' end of the strand, complementary to an existing template, as part of DNA replication.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

23 records
Show feature table
Start End DB Term Name
2 367 PIRSF PIRSF000804 DNA_pol_III_b
2 367 InterPro IPR001001 DNA polymerase III, beta sliding clamp
5 243 Gene3D G3DSA:3.10.150.10 DNA Polymerase III, subunit A, domain 2
139 365 Gene3D G3DSA:3.70.10.10 -
5 117 SUPERFAMILY SSF55979 DNA clamp
5 117 InterPro IPR046938 DNA clamp superfamily
247 366 Pfam PF02768 DNA polymerase III beta subunit, C-terminal domain
247 366 InterPro IPR022635 DNA polymerase III, beta sliding clamp, C-terminal
5 119 Pfam PF00712 DNA polymerase III beta subunit, N-terminal domain
5 119 InterPro IPR022634 DNA polymerase III, beta sliding clamp, N-terminal
246 367 SUPERFAMILY SSF55979 DNA clamp
246 367 InterPro IPR046938 DNA clamp superfamily
4 366 NCBIfam TIGR00663 DNA polymerase III subunit beta
4 366 InterPro IPR001001 DNA polymerase III, beta sliding clamp
4 366 CDD cd00140 beta_clamp
131 244 Pfam PF02767 DNA polymerase III beta subunit, central domain
131 244 InterPro IPR022637 DNA polymerase III, beta sliding clamp, central
128 245 SUPERFAMILY SSF55979 DNA clamp
128 245 InterPro IPR046938 DNA clamp superfamily
5 367 PANTHER PTHR30478 DNA POLYMERASE III SUBUNIT BETA
5 367 InterPro IPR001001 DNA polymerase III, beta sliding clamp
18 363 SMART SM00480 pol35
18 363 InterPro IPR001001 DNA polymerase III, beta sliding clamp

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 #9
0.957
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Surrounding area
Site 2 FPocket #5
0.409
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Surrounding area
Site 3 FPocket #3
0.217
Likely same site as P2Rank 3 4.0 Å 8 shared residues 80% of smaller site
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Surrounding area

Binding pockets · P2Rank

Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Site 1 P2Rank #1
0.05
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Surrounding area
Site 2 P2Rank #2
0.01
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Surrounding area
Site 3 P2Rank #3
0.002
Likely same site as FPocket 3 4.0 Å 8 shared residues 80% of smaller site
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Surrounding area
All structural evidence 0 experimental · 1 predicted

Structural evidence

0 + 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
AlphaFold DB HT085_RS00010
AlphaFold DB full sequence Viewing

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.

74 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 24 records from similar proteins
Structural ligands 19 0 loaded crystals
Measured bioactivity 5 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
0LA PDB via homolog 273.7 Da · LogP 4.16 · TPSA 53.1 Open detail RCSB PDB
1FL PDB via homolog Detail RCSB PDB
27O PDB via homolog Detail RCSB PDB
27R PDB via homolog Detail RCSB PDB
2HO 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
0LA RCSB PDB O25242 273.7 Da LogP 4.16 TPSA 53.1 ✓ Ro5 ✓ Clean C[C@@H](c1ccc2c3cc(ccc3[nH]c2c1)Cl)C(=O)O
1FL RCSB PDB O25242 250.2 Da LogP 3.04 TPSA 57.5 ✓ Ro5 ✓ Clean c1cc(c(cc1c2ccc(cc2F)F)C(=O)O)O
27O RCSB PDB P0A988 282.4 Da LogP 5.08 TPSA 37.3 1 viol. ✓ Clean C[C@H](c1ccc(c2c1cccc2)C3CCCCC3)C(=O)O
27R RCSB PDB P0A988 334.2 Da LogP 2.89 TPSA 80.4 ✓ Ro5 Alert c1cc(c(c(c1)C(=O)c2ccc(cc2)Br)N)CC(=O)O
2HO RCSB PDB P0A988 157.1 Da LogP 1.06 TPSA 43.1 ✓ Ro5 ✓ Clean c1cc(c(cc1C(=O)N)F)F
2HQ RCSB PDB P0A988 181.6 Da LogP 1.47 TPSA 46.2 ✓ Ro5 ✓ Clean c1cc2c(cc1Cl)C(=O)C(=O)N2
2HU RCSB PDB P0A988 162.1 Da LogP 2.08 TPSA 58.9 ✓ Ro5 ✓ Clean c1cc2c(cc[nH]2)cc1[N+](=O)[O-]
2J1 RCSB PDB P0A988 249.7 Da LogP 3.40 TPSA 53.1 ✓ Ro5 Alert c1c2c(cc(c1Cl)C(=O)O)[nH]c3c2CCCC3
2J2 RCSB PDB P0A988 249.7 Da LogP 3.33 TPSA 53.1 ✓ Ro5 ✓ Clean c1cc2c(cc1Cl)c3c([nH]2)[C@@H](CCC3)C(=O)O
322 RCSB PDB P0A988 499.2 Da LogP 3.17 TPSA 87.1 ✓ Ro5 Alert CCOc1cc(c(c(c1O)Br)Br)C[C@@H]2C(=O)N(C(=S)S2)CC…
323 RCSB PDB P0A988 414.5 Da LogP 2.48 TPSA 76.6 ✓ Ro5 ✓ Clean CN(C)c1ccc2c(c1)OC3=CC(=[N+](C)C)C=CC3=C2c4ccc(…
4FC RCSB PDB P0A988 216.2 Da LogP 3.19 TPSA 37.3 ✓ Ro5 ✓ Clean c1cc(ccc1c2ccc(cc2)F)C(=O)O
5CY RCSB PDB P0A988 471.7 Da LogP 5.62 TPSA 46.7 1 viol. ✓ Clean CC1(c2ccccc2[N+](=C1/C=C/C=C/C=C/3\C(c4ccccc4N3…
6NI RCSB PDB P0A988 163.1 Da LogP 1.47 TPSA 71.8 ✓ Ro5 ✓ Clean c1cc2cn[nH]c2cc1[N+](=O)[O-]
743 RCSB PDB P0A988 434.5 Da LogP 5.49 TPSA 79.5 1 viol. ✓ Clean CCCC(=NOCc1ccc(cc1)c2ccc(cc2)F)C3C(=O)CC(C(C3=O…
BU3 RCSB PDB P9WNU1 90.1 Da LogP -0.25 TPSA 40.5 ✓ Ro5 ✓ Clean C[C@H]([C@@H](C)O)O
MLU RCSB PDB P9WNU1 145.2 Da LogP 0.71 TPSA 49.3 ✓ Ro5 ✓ Clean CC(C)C[C@H](C(=O)O)NC
P4C RCSB PDB P0A988 324.4 Da LogP -0.72 TPSA 92.7 ✓ Ro5 ✓ Clean C(COCCOCCOCCOCCOCCOCC=O)O
SFK RCSB PDB P0A988 263.3 Da LogP 2.23 TPSA 66.4 ✓ Ro5 ✓ Clean CC(C)CCC(=O)N[C@@H](Cc1ccccc1)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.