Protein target profile

KP13_00998

hypothetical protein

Genome: KpKP13 Gene: AHE43472.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GVR0
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Length 199
Pocket druggability 0.233
Direct ligand evidence 0 55 total records
Functional annotation 1 EC 4 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 0.95. Structure available AlphaFold DB model + ColabFold model Review the complete evidence below

Risks to review

Microbiome similarity 234 of 4744 screened genomes (4.9%) have a significant similarity hit. Weak predicted binding pocket FPocket selected-pocket score 0.23.

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
4.9% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
N
DEG identity (%)
0.0 Higher values support similarity to known essential genes.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
95.7 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 0.233
Structure A0A0H3GVR0
Pocket Pocket 3
P2Rank 0.953
Structure A0A0H3GVR0
Pocket Pocket 1
ColabFold model
FPocket 0.141 · Pocket 5
P2Rank 0.952 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 234 / 4744 genomes with a hit
Prevalence 4.9%

Cross-references

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

Sequence

UniProt A0A0H3GVR0

Sequence

Primary amino-acid sequence viewer.

MSQSHFFAHLSRLKLINRWPLMRNVRTENVSEHSLQVAMVAHALAAIKNRKFGGQVNAERIALLAMYHDASEVLTGDLPTPVKYFNSQIAQEYKAIEKIAQQKLVEMVPDELRDIFEPLIDEHHYSEEEQSIVKQADALCAYLKCLEELSAGNNEFLLAKGRLEKTLASRRSAEMDYFMQVFVPSFQLSLDEISQDSPL

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

4
  • GO:0002953 Catalysis of the reaction: a 2'-deoxyribonucleoside 5'-phosphate + H2O = a 2'-deoxyribonucleoside + phosphate.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0046872 Binding to a metal ion.
  • GO:0000166 Binding to a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

14 records
Show feature table
Start End DB Term Name
26 151 SMART SM00471 hd_13
26 151 InterPro IPR003607 HD/PDEase domain
3 195 Hamap MF_01100 5'-deoxynucleotidase YfbR [yfbR].
3 195 InterPro IPR022971 5'-deoxynucleotidase YfbR
5 186 Pfam PF12917 5'-deoxynucleotidase YfbR-like
3 185 SUPERFAMILY SSF109604 HD-domain/PDEase-like
1 199 Gene3D G3DSA:1.10.3210.10 Hypothetical protein af1432
28 124 CDD cd00077 HDc
28 124 InterPro IPR003607 HD/PDEase domain
5 154 PANTHER PTHR11845 UNCHARACTERIZED
5 154 InterPro IPR039356 5'-deoxynucleotidase YfbR/HDDC2
30 142 ProSiteProfiles PS51831 HD domain profile.
30 142 InterPro IPR006674 HD domain
1 199 FunFam G3DSA:1.10.3210.10:FF:000002 Nucleotidase YfbR

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 #3
0.233
Likely same site as P2Rank 1 5.7 Å 20 shared residues 87% of smaller site
Unusual size
Show in viewer
Surrounding area

Binding pockets · P2Rank

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

Site 1 P2Rank #1
0.953
Likely same site as FPocket 3 5.7 Å 20 shared residues 87% of smaller site
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.044
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.016
Show in viewer
Surrounding area
Residue sets
UniProt: Binding site:137-137
UniProt: Binding site:18-19
UniProt: Binding site:33-33
UniProt: Binding site:68-68
UniProt: Binding site:69-69
UniProt: Binding site:77-80
UniProt: Site:18-18 Appears to be important in orienting the phosphate for catalysis
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_A0A0H3GVR0
AlphaFold DB — — full sequence — Viewing
ColabFold KP13_00998
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.

55 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 5 records from similar proteins
Structural ligands 5 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
7D3 PDB via homolog 411.2 Da · LogP -0.86 · TPSA 212.4 Open detail RCSB PDB
7D4 PDB via homolog Detail RCSB PDB
7D5 PDB via homolog Detail RCSB PDB
7D7 PDB via homolog Detail RCSB PDB
D5M 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
7D3 RCSB PDB
5TK6
O24769 411.2 Da LogP -0.86 TPSA 212.4 1 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@H](O3)COP(=O)…
7D4 RCSB PDB
5TK7
O24769 491.2 Da LogP -0.74 TPSA 258.9 2 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@H](O3)COP(=O)…
7D5 RCSB PDB
5TK8
O24769 331.2 Da LogP -0.98 TPSA 165.8 ✓ Ro5 ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@H](O3)COP(=O)…
7D7 RCSB PDB
5TK9
O24769 251.2 Da LogP -1.09 TPSA 119.3 ✓ Ro5 ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@H](O3)CO)CO)N
D5M RCSB PDB
2PAU
P76491 331.2 Da LogP -0.83 TPSA 165.8 ✓ Ro5 ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3C[C@@H]([C@H](O3)COP(=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.