KpKP13 Protein target profile

Non-specific ribonucleoside hydrolase rihC

Accession: KP13_01970

Gene: rihC AHE46409.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GJ10
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Length 304
Pocket druggability (P2Rank · AlphaFold DB model) 0.769
Direct ligand evidence 0 56 total records
Functional annotation 1 EC 7 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.

Main supporting evidence

No similar human protein detected The current BLAST sequence screen did not find a significant human match, lowering apparent off-target risk. Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Second pocket predictor agrees P2Rank predicted binding-site probability 0.77. Structure available AlphaFold DB model + ColabFold model Review the complete evidence below

Risks to review

Microbiome similarity 96 of 4744 screened genomes (2.0%) have a significant similarity hit. This target also has a predicted binding pocket (P2Rank 0.77) — check the ligand evidence before deprioritizing on off-target risk alone. Weak predicted binding pocket FPocket selected-pocket score 0.24.

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
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 (%)
82.566 Higher values support similarity to known essential genes.
DEG E-value
8.39e-178 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
97.3 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) 0.769
Structure A0A0H3GJ10
Pocket Pocket 1
Druggability (FPocket) 0.244
Structure A0A0H3GJ10
Pocket Pocket 1
ColabFold model
P2Rank 0.833 · Pocket 1
FPocket 0.282 · Pocket 1
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.

MRLPIILDTDPGIDDAAAIAAALFAPELDLQLMTTVAGNVSVEKTTRNALQLLHFWNADVPLAQGASMPLVRPLRDAASVHGESGMEGYDFVEHQRQPLAKPAFQAIRDALMHAAEPITLVAIGPLTNIALLLTQYPECVFNIRRLVIMGGSAGRGNFTPNAEFNIAIDPEAAAKVFHSGLEIVMCGLDVTNRALLAADYLATLPTLNQTGKMLHALFSHYRSGSMSSGLRMHDLCAIAWLARPELFTLQPCFVAVETQGTWTAGTTVVDIEGRLGQPANAQVALDIDVEGFQRWAAEVIALAP

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Subcellular localization

Localization
Unknown

Enzyme Commission (EC)

1

Gene Ontology (GO)

7
  • GO:0016798 Catalysis of the hydrolysis of any glycosyl bond.
  • GO:0016799 Catalysis of the hydrolysis of any N-glycosyl bond.
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0008477 Catalysis of the reaction: a N-D-ribosylpurine + H2O = a purine + D-ribose.
  • GO:0006144 The chemical reactions and pathways involving purine nucleobases, one of the two classes of nitrogen-containing ring compounds found in DNA and RNA, which include adenine and guanine.
  • GO:0006152 The chemical reactions and pathways resulting in the breakdown of purine nucleoside, one of a family of organic molecules consisting of a purine base covalently bonded to a sugar ribose (a ribonucleoside) or deoxyribose (a deoxyribonucleoside).
  • GO:0006206 The chemical reactions and pathways involving pyrimidine nucleobases, 1,3-diazine, organic nitrogenous bases.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

12 records
Show feature table
Start End DB Term Name
4 296 PANTHER PTHR12304 INOSINE-URIDINE PREFERRING NUCLEOSIDE HYDROLASE
4 296 InterPro IPR023186 Inosine/uridine-preferring nucleoside hydrolase
2 302 Gene3D G3DSA:3.90.245.10 -
2 302 InterPro IPR036452 Ribonucleoside hydrolase-like
4 300 CDD cd02651 nuc_hydro_IU_UC_XIUA
2 302 FunFam G3DSA:3.90.245.10:FF:000002 Non-specific ribonucleoside hydrolase RihC
3 299 SUPERFAMILY SSF53590 Nucleoside hydrolase
3 299 InterPro IPR036452 Ribonucleoside hydrolase-like
1 304 Hamap MF_01432 Non-specific ribonucleoside hydrolase RihC [rihC].
1 304 InterPro IPR022976 Non-specific ribonucleoside hydrolase RihC
5 293 Pfam PF01156 Inosine-uridine preferring nucleoside hydrolase
5 293 InterPro IPR001910 Inosine/uridine-preferring nucleoside hydrolase 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.

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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
0.769
Likely same site as FPocket 1 0.7 Å 18 shared residues 95% of smaller site
Show in viewer
Surrounding area

Binding pockets · FPocket

Druggability (FPocket): high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Pocket 1 FPocket #1
0.244
Likely same site as P2Rank 1 0.7 Å 18 shared residues 95% of smaller site
Show in viewer
Surrounding area
Residue sets
UniProt: Active site:233-233
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_A0A0H3GJ10
AlphaFold DB — — full sequence — Viewing
ColabFold KP13_01970
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.

56 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 6 records from similar proteins
Structural ligands 5 0 loaded crystals
Measured bioactivity 1 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
DNB PDB via homolog 239.3 Da · LogP -1.42 · TPSA 124.8 Open detail RCSB PDB
IMH PDB via homolog Detail RCSB PDB
NOS PDB via homolog Detail RCSB PDB
PIR PDB via homolog Detail RCSB PDB
TAM 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
DNB RCSB PDB
3MKN
C3T3U2 239.3 Da LogP -1.42 TPSA 124.8 1 viol. ✓ Clean c1cc(c(cc1[C@H]2[C@@H]([C@@H]([C@H](N2)CO)O)O)N…
IMH RCSB PDB
6ZK5
B6T563 266.3 Da LogP -2.02 TPSA 134.3 1 viol. ✓ Clean c1c(c2c([nH]1)C(=O)NC=N2)[C@H]3[C@@H]([C@@H]([C…
NOS RCSB PDB
3B9X
P33022 268.2 Da LogP -2.27 TPSA 133.5 ✓ Ro5 ✓ Clean c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO)O)O)N=…
PIR RCSB PDB
2MAS
Q27546 224.3 Da LogP -1.00 TPSA 98.7 ✓ Ro5 ✓ Clean c1cc(ccc1[C@H]2[C@@H]([C@@H]([C@H](N2)CO)O)O)N
TAM RCSB PDB
3B9X
P33022 163.2 Da LogP -1.17 TPSA 86.7 ✓ Ro5 ✓ Clean C(CO)C(CCO)(CCO)N

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.

Sequence

UniProt A0A0H3GJ10

Chemistry

ChEMBL CHEMBL3827395