Protein target profile

KP13_32218

Transcription termination factor rho

Genome: KpKP13 Gene: rho AHE47004.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GH32
Length 443
Pocket druggability 0.332
Direct ligand evidence 0 61 total records
Functional annotation 1 EC 9 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 similarity
56.0% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
98.871 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
91.29 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 0.332
Structure A0A0H3GH32
Pocket Pocket 5
P2Rank 0.093
Structure A0A0H3GH32
Pocket Pocket 1
ColabFold model
FPocket 0.28 · Pocket 3
P2Rank 0.303 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 2656 / 4744 genomes with a hit
Prevalence 56.0%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MEVPAIPFTTLSSRFTPSLRTHTTMNLTELKNTPVSELITLGENMGLENLARMRKQDIIFAILKQHSKSGEDIFGDGVLEILQDGFGFLRSADSSYLAGPDDIYVSPSQIRRFNLRTGDTISGKIRPPKEGERYFALLKVNEVNYDKPENARNKILFENLTPLHANSRLRMERGNGSTEDLTARVLDLASPIGRGQRGLIVAPPKAGKTMLLQNIAQSIAYNHPDCVLMVLLIDERPEEVTEMQRLVKGEVVASTFDEPASRHVQVAEMVIEKAKRLVEHKKDVIILLDSITRLARAYNTVVPASGKVLTGGVDANALHRPKRFFGAARNVEEGGSLTIIATALIDTGSKMDEVIYEEFKGTGNMELHLSRKIAEKRVFPAIDYNRSGTRKEELLTTQEELQKMWILRKIIHPMGEIDAMEFLINKLAMTKTNDDFFDMMKRS

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 9 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

9
  • GO:0016887 Catalysis of the reaction: ATP + H2O = ADP + H+ phosphate. ATP hydrolysis is used in some reactions as an energy source, for example to catalyze a reaction or drive transport against a concentration gradient.
  • GO:0003676 Binding to a nucleic acid.
  • GO:0008186 Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction requires the presence of RNA, and it drives another reaction.
  • GO:0003723 Binding to an RNA molecule or a portion thereof.
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0006353 The completion of transcription: the RNA polymerase pauses, the RNA-DNA hybrid dissociates, followed by the release of the RNA polymerase from its DNA template.
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0004386 Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive the unwinding of a DNA or RNA helix.
  • GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

37 records
Show feature table
Start End DB Term Name
154 443 FunFam G3DSA:3.40.50.300:FF:000072 Transcription termination factor Rho
22 442 PANTHER PTHR46425 TRANSCRIPTION TERMINATION FACTOR RHO
22 442 InterPro IPR004665 Transcription termination factor Rho
29 71 SMART SM00959 Rho_N_2_a
29 71 InterPro IPR011112 Rho termination factor, N-terminal
75 142 CDD cd04459 Rho_CSD
75 142 InterPro IPR011113 Rho termination factor, RNA-binding domain
25 71 FunFam G3DSA:1.10.720.10:FF:000001 Transcription termination factor Rho
23 71 Gene3D G3DSA:1.10.720.10 -
72 147 ProSiteProfiles PS51856 Rho RNA-binding domain profile.
72 147 InterPro IPR011113 Rho termination factor, RNA-binding domain
114 395 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
114 395 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
154 443 Gene3D G3DSA:3.40.50.300 -
154 443 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
1 443 Hamap MF_01884 Transcription termination factor Rho [rho].
1 443 InterPro IPR004665 Transcription termination factor Rho
76 149 Pfam PF07497 Rho termination factor, RNA-binding domain
76 149 InterPro IPR011113 Rho termination factor, RNA-binding domain
26 441 NCBIfam TIGR00767 transcription termination factor Rho
26 441 InterPro IPR004665 Transcription termination factor Rho
72 149 SUPERFAMILY SSF50249 Nucleic acid-binding proteins
72 149 InterPro IPR012340 Nucleic acid-binding, OB-fold
72 146 Gene3D G3DSA:2.40.50.140 -
72 146 InterPro IPR012340 Nucleic acid-binding, OB-fold
184 387 Pfam PF00006 ATP synthase alpha/beta family, nucleotide-binding domain
184 387 InterPro IPR000194 ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain
25 70 SUPERFAMILY SSF68912 Rho N-terminal domain-like
25 70 InterPro IPR036269 Rho termination factor, N-terminal domain superfamily
72 146 FunFam G3DSA:2.40.50.140:FF:000010 Transcription termination factor Rho
194 379 SMART SM00382 AAA_5
194 379 InterPro IPR003593 AAA+ ATPase domain
29 71 Pfam PF07498 Rho termination factor, N-terminal domain
180 428 CDD cd01128 rho_factor_C
180 428 InterPro IPR041703 Transcription termination factor Rho, ATP binding domain
76 142 SMART SM00357 csp_8
76 142 InterPro IPR011129 Cold shock domain

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

Loading 3D structure...

Drag to rotate — click the view, then scroll to zoom.

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 #5
0.332
Show in viewer
Surrounding area
Site 2 FPocket #10
0.275
Show in viewer
Surrounding area

Binding pockets · P2Rank

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

Site 1 P2Rank #1
0.093
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.049
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.04
Show in viewer
Surrounding area
Site 4 P2Rank #4
0.031
Show in viewer
Surrounding area
Site 5 P2Rank #5
0.018
Show in viewer
Surrounding area
Residue sets
UniProt: Binding site:169-174
UniProt: Binding site:181-186
UniProt: Binding site:212-212
UniProt: Site:326-326 RNA-binding 2
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_A0A0H3GH32
AlphaFold DB full sequence Viewing
ColabFold KP13_32218
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.

61 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 11 records from similar proteins
Structural ligands 11 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
AF3 PDB via homolog 84.0 Da · LogP 0.88 · TPSA 0.0 Open detail RCSB PDB
AGS PDB via homolog Detail RCSB PDB
ANP PDB via homolog Detail RCSB PDB
BCM PDB via homolog Detail RCSB PDB
BEF 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
AF3 RCSB PDB B7UMA6 84.0 Da LogP 0.88 TPSA 0.0 ✓ Ro5 ✓ Clean F[Al](F)F
AGS RCSB PDB P0AG30 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)…
ANP RCSB PDB P0AG30 506.2 Da LogP -2.06 TPSA 281.9 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
BCM RCSB PDB P0AG30 302.3 Da LogP -3.30 TPSA 148.3 1 viol. ✓ Clean C[C@](CO)([C@@H]([C@@]12C(=O)N[C@@](C(=C)CCO1)(…
BEF RCSB PDB P0AG30 66.0 Da LogP 0.88 TPSA 0.0 ✓ Ro5 ✓ Clean [Be-](F)(F)F
DG RCSB PDB P0AG30 347.2 Da LogP -1.54 TPSA 185.8 ✓ Ro5 ✓ Clean c1nc2c(n1[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O)N…
DT RCSB PDB P0AG30 322.2 Da LogP -1.40 TPSA 151.1 ✓ Ro5 ✓ Clean CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O…
FB RCSB PDB P0AG30 330.3 Da LogP -3.73 TPSA 165.4 1 viol. ✓ Clean C[C@](CO)([C@@H]([C@@]12C(=O)N[C@@](C(=CC=O)CCO…
FPD RCSB PDB P0AG30 440.5 Da LogP -1.64 TPSA 165.4 1 viol. ✓ Clean C[C@](CO)([C@@H]([C@@]12C(=O)N[C@@]([C@@H](CCO1…
IUM RCSB PDB P38527 270.0 Da LogP -2.38 TPSA 46.1 ✓ Ro5 ✓ Clean [O-][U+4][O-]
SPD RCSB PDB P0AG30 145.2 Da LogP -0.34 TPSA 64.1 ✓ Ro5 ✓ Clean C(CCNCCCN)CN

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.