KpKP13 Protein target profile

Sorbitol-6-phosphate 2-dehydrogenase

Accession: KP13_02593

Gene: srlD AHE43055.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3H1W1
Length 259
Pocket druggability (P2Rank · AlphaFold DB model) 0.897
Direct ligand evidence 0 57 total records
Functional annotation 0 EC 2 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 (%)
35.484 Lower values reduce human off-target concern.
Human E-value
5.54e-06
Gut microbiome similarity
1.6% 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
96.98 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) 0.897
Structure A0A0H3H1W1
Pocket Pocket 1
Druggability (FPocket) 0.784
Structure A0A0H3H1W1
Pocket Pocket 14
ColabFold model
P2Rank 0.955 · Pocket 1
FPocket 0.565 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 76 / 4744 genomes with a hit
Prevalence 1.6%

Sequence

Primary amino-acid sequence viewer.

MNQVAVVIGGGQTLGEFLCRGLAAEGYRVAVVDIQSEKASRVAQEINAEYGEGMAYGFGADATSEASVTALAHGVDEIFSRVDLLVYSAGIAKAAFISDFALGDFDRSLQVNLVGYFLCAREFSRLMIRDGIKGRIIQINSKSGKVGSKHNSGYSAAKFGGVGLTQSLALDLAEYGITVHSLMLGNLLKSPMFQSLLPQYATKLGIDESEVEQYYIDKVPLKRGCEYQDVLNVLMFYASPQASYCTGQSINVTGGQVMF

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 GO

Subcellular localization

Localization
Cytoplasmic

Gene Ontology (GO)

2
  • GO:0016491 Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
  • GO:0016616 Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces NAD+ or NADP.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

24 records
Show feature table
Start End DB Term Name
128 144 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature
128 144 InterPro IPR002347 Short-chain dehydrogenase/reductase SDR
4 21 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature
4 21 InterPro IPR002347 Short-chain dehydrogenase/reductase SDR
220 240 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature
220 240 InterPro IPR002347 Short-chain dehydrogenase/reductase SDR
80 91 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature
80 91 InterPro IPR002347 Short-chain dehydrogenase/reductase SDR
154 173 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature
154 173 InterPro IPR002347 Short-chain dehydrogenase/reductase SDR
141 169 ProSitePatterns PS00061 Short-chain dehydrogenases/reductases family signature.
141 169 InterPro IPR020904 Short-chain dehydrogenase/reductase, conserved site
2 258 Gene3D G3DSA:3.40.50.720 -
2 258 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains
2 258 InterPro IPR036291 NAD(P)-binding domain superfamily
134 142 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature
134 142 InterPro IPR002347 Short-chain dehydrogenase/reductase SDR
80 91 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature
154 173 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature
3 197 Pfam PF00106 short chain dehydrogenase
3 197 InterPro IPR002347 Short-chain dehydrogenase/reductase SDR
2 256 PANTHER PTHR42760 SHORT-CHAIN DEHYDROGENASES/REDUCTASES FAMILY MEMBER
1 258 CDD cd05322 SDH_SDR_c_like
2 258 FunFam G3DSA:3.40.50.720:FF:000091 Sorbitol-6-phosphate dehydrogenase

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
0.897
Likely same site as FPocket 4 6.5 Å 27 shared residues 77% of smaller site
Show in viewer
Surrounding area
Pocket 2 P2Rank #2
0.321
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #14
0.784
Show in viewer
Surrounding area
Pocket 2 FPocket #4
0.591 Unusual size
Likely same site as P2Rank 1 6.5 Å 27 shared residues 77% of smaller site
Show in viewer
Surrounding area
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_A0A0H3H1W1
AlphaFold DB full sequence Viewing
ColabFold KP13_02593
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.

57 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 7 records from similar proteins
Structural ligands 7 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
1HS PDB via homolog 200.3 Da · LogP -0.01 · TPSA 74.6 Open detail RCSB PDB
AAE PDB via homolog Detail RCSB PDB
AOI PDB via homolog Detail RCSB PDB
CHO PDB via homolog Detail RCSB PDB
EMO 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
1HS RCSB PDB A7IQH5 200.3 Da LogP -0.01 TPSA 74.6 ✓ Ro5 ✓ Clean C[C@@H](CSCCS(=O)(=O)O)O
AAE RCSB PDB A0A1E3M3N6 102.1 Da LogP 0.05 TPSA 54.4 ✓ Ro5 ✓ Clean CC(=O)CC(=O)O
AOI RCSB PDB P9WGT1 290.4 Da LogP 3.96 TPSA 37.3 ✓ Ro5 ✓ Clean C[C@]12CC[C@H](C[C@@H]1CC[C@@H]3[C@@H]2CC[C@]4(…
CHO RCSB PDB P0AET8 449.6 Da LogP 3.59 TPSA 106.9 ✓ Ro5 ✓ Clean C[C@H](CCC(=O)NCC(=O)O)[C@H]1CC[C@@H]2[C@@]1(CC…
EMO RCSB PDB P16544 270.2 Da LogP 1.89 TPSA 94.8 ✓ Ro5 Alert Cc1cc2c(c(c1)O)C(=O)c3c(cc(cc3O)O)C2=O
ISZ RCSB PDB P16544 135.1 Da LogP 1.25 TPSA 66.2 ✓ Ro5 Alert [H]/N=N/C(=O)c1ccncc1
QT8 RCSB PDB A0A1E3M3N6 116.1 Da LogP 0.44 TPSA 54.4 ✓ Ro5 ✓ Clean CCC(=O)CC(=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.