KpATCC43816 Protein target profile

NAD-dependent glycerol-3-phosphate dehydrogenasefamily protein

Accession: VK055_0795

Gene: AIK79418.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3GNC1
Length 291
Pocket druggability (P2Rank · AlphaFold DB model) 0.915
Direct ligand evidence 0 60 total records
Functional annotation 0 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.

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 (%)
29.021 Lower values reduce human off-target concern.
Human E-value
2.21e-32
Gut microbiome similarity
0.4% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Structure confidence

ColabFold pLDDT
96.51 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) 0.915
Structure A0A0H3GNC1
Pocket Pocket 1
Druggability (FPocket) 0.917
Structure A0A0H3GNC1
Pocket Pocket 7
ColabFold model
P2Rank 0.904 · Pocket 1
FPocket 0.915 · Pocket 11
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 18 / 4744 genomes with a hit
Prevalence 0.4%

Metabolic context

Reactions catalyzed, pathway membership, and centrality in the genome-scale metabolic network.

This protein is not associated with the imported metabolic network for this genome.

Browse the genome's metabolic network

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MSTLPKVAVLGLGAMGHAFASNLLKNGFTVAGWNRSPARGEDLQAHGLSLHATPQQSVADAEVIISMLADGEATLEVLAQIAPACQPQAIYCQMGTIGLPETRQAIALLRELQPAMTYIDAPVSGTKAPAEKAQILVLASGDREKGAAAEPVFAAISRGTQWFGEAGNSQKMKLVLNAWLISMMQGIAESAQLAKTLGFTPDQLWSALEGGPLAAPYVKVKLDAIASEQFTPQMQLAHALKDARLALSLAEPHTMPGLETIAELWQQAADAGYAGEDLSAVYQWLSPSSKA

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 GO

Subcellular localization

Localization
Periplasmic

Gene Ontology (GO)

4
  • GO:0050661 Binding to nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH.
  • GO:0051287 Binding to nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
  • 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.

21 records
Show feature table
Start End DB Term Name
1 164 Gene3D G3DSA:3.40.50.720 -
165 286 SUPERFAMILY SSF48179 6-phosphogluconate dehydrogenase C-terminal domain-like
165 286 InterPro IPR008927 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily
1 20 Phobius SIGNAL_PEPTIDE Signal peptide region
7 15 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
16 20 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
166 290 Gene3D G3DSA:1.10.1040.10 -
166 290 InterPro IPR013328 6-phosphogluconate dehydrogenase, domain 2
4 284 PANTHER PTHR43580 OXIDOREDUCTASE GLYR1-RELATED
167 285 Pfam PF14833 NAD-binding of NADP-dependent 3-hydroxyisobutyrate dehydrogenase
167 285 InterPro IPR029154 3-hydroxyisobutyrate dehydrogenase-like, NAD-binding domain
1 20 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM
1 20 SignalP_GRAM_NEGATIVE SignalP-noTM SignalP-noTM
21 291 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
6 165 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains
6 165 InterPro IPR036291 NAD(P)-binding domain superfamily
6 162 Pfam PF03446 NAD binding domain of 6-phosphogluconate dehydrogenase
6 162 InterPro IPR006115 6-phosphogluconate dehydrogenase, NADP-binding
1 6 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
1 291 PIRSF PIRSF000103 HIBADH
1 291 InterPro IPR015815 3-hydroxyisobutyrate dehydrogenase-related

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

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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
0.915
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #7
0.917
Show in viewer
Surrounding area
Residue sets
UniProt: Active site:173-173
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_A0A0H3GNC1
AlphaFold DB full sequence Viewing
ColabFold VK055_0795
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.

60 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 10 records from similar proteins
Structural ligands 10 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
3OH PDB via homolog 90.1 Da · LogP -0.55 · TPSA 57.5 Open detail RCSB PDB
9ON PDB via homolog Detail RCSB PDB
AKR PDB via homolog Detail RCSB PDB
BO3 PDB via homolog Detail RCSB PDB
HIU 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
3OH RCSB PDB P9WNY5 90.1 Da LogP -0.55 TPSA 57.5 ✓ Ro5 ✓ Clean C(CO)C(=O)O
9ON RCSB PDB P9WNY5 146.1 Da LogP 0.57 TPSA 74.6 ✓ Ro5 ✓ Clean C[C@@H](CCC(=O)O)C(=O)O
AKR RCSB PDB P9WNY5 72.1 Da LogP 0.26 TPSA 37.3 ✓ Ro5 ✓ Clean C=CC(=O)O
BO3 RCSB PDB P0A9V8 61.8 Da LogP -2.05 TPSA 60.7 ✓ Ro5 ✓ Clean B(O)(O)O
HIU RCSB PDB P9WNY5 104.1 Da LogP -0.30 TPSA 57.5 ✓ Ro5 ✓ Clean C[C@H](CO)C(=O)O
HUI RCSB PDB P9WNY5 104.1 Da LogP -0.30 TPSA 57.5 ✓ Ro5 ✓ Clean C[C@@H](CO)C(=O)O
LLQ RCSB PDB P0A9V8 156.2 Da LogP -1.77 TPSA 94.8 ✓ Ro5 ✓ Clean C([C@@H](CS(=O)(=O)O)O)O
LW7 RCSB PDB D3Q3R0 235.3 Da LogP 3.66 TPSA 12.4 ✓ Ro5 ✓ Clean c1ccc(cc1)CCC2=NCCc3c2cccc3
LW9 RCSB PDB D3Q3R0 128.3 Da LogP 3.61 TPSA 0.0 ✓ Ro5 ✓ Clean CCCCC(CC)CC
TLA RCSB PDB A3MU08 150.1 Da LogP -2.12 TPSA 115.1 ✓ Ro5 ✓ Clean [C@@H]([C@H](C(=O)O)O)(C(=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.