KpKP13 Protein target profile

putative carbohydrate kinase

Accession: KP13_05552

Gene: AHE44558.1 3D evidence: Experimental + ColabFold model UniProt A6T989
Length 290
Pocket druggability (P2Rank · Experimental) 0.948
Direct ligand evidence 0 56 total records
Functional annotation 0 EC 3 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
Hit
Human identity (%)
28.276 Lower values reduce human off-target concern.
Human E-value
1.24e-21
Gut microbiome similarity
0.2% 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.

Structure confidence

ColabFold pLDDT
95.75 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

PDB experimental structure

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) 0.948
Structure 3IKH
Pocket Pocket 1
Druggability (FPocket) 0.796
Structure 3I3Y
Pocket Pocket 1
ColabFold model
P2Rank 0.959 · Pocket 1
FPocket 0.723 · Pocket 10
Core conservation Accessory gene
Roary accessory
CoreCruncher accessory
Gut microbiome 10 / 4744 genomes with a hit
Prevalence 0.2%

Sequence

Primary amino-acid sequence viewer.

MRVYVTGNITVDETWSIPDIPKKGASIHGVKVSQDIGGKGANQAIILSRCGIETRLIAATGNDSNGAWIRQQIKNEPLTLLPDGHFNQHSDTSIILNSADGDNAIITTTAAADTFSLDEMIPHMADAVAGDILLQQGNFSLDKTRALFQYARSRGMTTVFNPSPVNPDFCHLWPLIDIAVVNESEAELLQPYGVKTLVITQGAAGAWLVQEGLRQFCPAVPAEALDTTGAGDTFLAVMLASALLRGVAPDALALAHASRAAAITVSRRGTLSAFPGSRELAALLTTDGAR

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

3 GO

Subcellular localization

Localization
Cytoplasmic

Gene Ontology (GO)

3
  • GO:0016301 Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
  • GO:0006014 The chemical reactions and pathways involving D-ribose (ribo-pentose). As beta-D-ribofuranose, D-ribose forms the glycose group of all ribonucleosides, ribonucleotides and ribonucleic acids, and also of ribose phosphates, various glycosides, some coenzymes and some forms of vitamin B12.
  • GO:0004747 Catalysis of the reaction: ATP + D-ribose = ADP + D-ribose 5-phosphate.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

21 records
Show feature table
Start End DB Term Name
1 282 Hamap MF_01987 Ribokinase [rbsK].
1 282 InterPro IPR011877 Ribokinase
1 284 SUPERFAMILY SSF53613 Ribokinase-like
1 284 InterPro IPR029056 Ribokinase-like
37 61 ProSitePatterns PS00583 pfkB family of carbohydrate kinases signature 1.
37 61 InterPro IPR002173 Carbohydrate/purine kinase, PfkB, conserved site
1 284 PANTHER PTHR10584 SUGAR KINASE
5 26 PRINTS PR00990 Ribokinase signature
5 26 InterPro IPR002139 Ribokinase/fructokinase
197 208 PRINTS PR00990 Ribokinase signature
197 208 InterPro IPR002139 Ribokinase/fructokinase
103 116 PRINTS PR00990 Ribokinase signature
103 116 InterPro IPR002139 Ribokinase/fructokinase
171 186 PRINTS PR00990 Ribokinase signature
171 186 InterPro IPR002139 Ribokinase/fructokinase
32 51 PRINTS PR00990 Ribokinase signature
32 51 InterPro IPR002139 Ribokinase/fructokinase
1 289 Gene3D G3DSA:3.40.1190.20 -
1 289 InterPro IPR029056 Ribokinase-like
24 272 Pfam PF00294 pfkB family carbohydrate kinase
24 272 InterPro IPR011611 Carbohydrate kinase PfkB

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

Pocket 1 FPocket #1
0.796
Show in viewer
Surrounding area
All structural evidence 2 experimental · 1 predicted

Structural evidence

2 + 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
PDB 3I3Y
X-ray A Viewing
PDB 3IKH
X-ray A Loaded
ColabFold KP13_05552
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 ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 6 records from similar proteins
Structural ligands 6 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
A12 PDB via homolog 425.2 Da · LogP -1.64 · TPSA 223.4 Open detail RCSB PDB
ACP PDB via homolog Detail RCSB PDB
AN2 PDB via homolog Detail RCSB PDB
KDG PDB via homolog Detail RCSB PDB
RAH 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
A12 RCSB PDB Q9H477 425.2 Da LogP -1.64 TPSA 223.4 2 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
ACP RCSB PDB A0A3S7X0F5 505.2 Da LogP -1.52 TPSA 269.9 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
AN2 RCSB PDB Q9H477 426.2 Da LogP -1.78 TPSA 238.4 2 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
KDG RCSB PDB Q53W83 178.1 Da LogP -2.26 TPSA 115.1 ✓ Ro5 ✓ Clean C([C@@H]([C@@H](CO)O)O)C(=O)C(=O)O
RAH RCSB PDB P32143 324.2 Da LogP -3.21 TPSA 191.0 1 viol. ✓ Clean C([C@@H]1[C@H]([C@@H]([C@](O1)(COP(=O)(O)O)O)O)…
RIB RCSB PDB A1A6H3 150.1 Da LogP -2.58 TPSA 90.2 ✓ Ro5 ✓ Clean C([C@@H]1[C@H]([C@H]([C@H](O1)O)O)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.

Cross-references

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