KpATCC43816 Protein target profile

Quinate/shikimate dehydrogenase, NAD(P)-dependent

Accession: VK055_2498

Gene: ydiB AIK81095.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism 4 reactions UniProt A0A0H3GJ74
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Length 287
Pocket druggability (P2Rank · AlphaFold DB model) 0.89
Metabolic reactions 4
Chokepoint Yes
Direct ligand evidence 0 55 total records
Functional annotation 1 EC 6 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

Metabolic chokepoint Catalyzes a reaction that is the only producer or consumer of a metabolite in the imported metabolic model. Central metabolic position More central than 99.1% of genes in this genome. No similar human protein detected The current BLAST sequence screen did not find a significant human match, lowering apparent off-target risk. Second pocket predictor agrees P2Rank predicted binding-site probability 0.89. Review the complete evidence below

Risks to review

Microbiome similarity 369 of 4744 screened genomes (7.8%) have a significant similarity hit. This target also has a predicted binding pocket (P2Rank 0.89) — check the ligand evidence before deprioritizing on off-target risk alone. Mixed conservation Core/accessory calls are not fully concordant. Weak predicted binding pocket FPocket selected-pocket score 0.31.

Evidence coverage

Core evidence streams are available for this target.
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
7.8% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
51.418 Higher values support similarity to known essential genes.
DEG E-value
3.42e-110 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
97.01 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) 0.89
Structure A0A0H3GJ74
Pocket Pocket 1
Druggability (FPocket) 0.312
Structure A0A0H3GJ74
Pocket Pocket 6
ColabFold model
P2Rank 0.892 · Pocket 1
FPocket 0.431 · Pocket 14
Core conservation Accessory gene
Roary core
CoreCruncher accessory
Gut microbiome 369 / 4744 genomes with a hit
Prevalence 7.8%

Metabolic context

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

Explore metabolic network

Attractive metabolic target: catalyzes a producing chokepoint reaction in Phenylalanine, tyrosine and tryptophan biosynthesis, more central than 99.1% of genes in this genome, no human homolog detected.

Relative network centrality 99.1% more central than 99.1% of genes in this genome
Chokepoint Chokepoint gene
Pathways
Phenylalanine, tyrosine and tryptophan biosynthesis
Catalyzed reactions

4 reactions mapped to this gene in the metabolic model. Open the full network to see each one, with substrates/products and the reaction-reaction map.

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MAERITGHTELIGLIATPIRHSMSPTMHNEAFAHLGLDYVYLAFEVGNQELKDVVQGFRAMKLRGFNVSMPNKTEICQYLDKLSPAAQLVGAVNTVVNDDGVLTGHITDGTGYMRALSEAGIDIIGKKMTVLGAGGAATALCVQAALDGVKAISIFNRRDKFFANAEETVAKIRHNTDCEIHLFDLDDHDKLRAEIDSSVILTNATGVGMKPFEGQMLLPDDSFLRPDLIVSDVVYNPRKTHLLEVAEKKGCRTLNGLGMMLWQGARAFEIWTGKQMPVDYIKSILF

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Subcellular localization

Localization
Cytoplasmic

Enzyme Commission (EC)

1

Gene Ontology (GO)

6
  • GO:0004764 Catalysis of the reaction: shikimate + NADP+ = 3-dehydroshikimate + NADPH + H+.
  • 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:0019632 The chemical reactions and pathways involving shikimate, (3R,4S,5R)--3,4,5-trihydroxycyclohex-1-ene-1-carboxylate, the anion of shikimic acid. It is an important intermediate in the biosynthesis of aromatic amino acids.
  • GO:0008652 The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
  • GO:0009073 The chemical reactions and pathways resulting in the formation of aromatic amino acid family, amino acids with aromatic ring (phenylalanine, tyrosine, tryptophan).
  • GO:0009423 The chemical reactions and pathways resulting in the formation of the unsymmetrical ether derived from phosphoenolpyruvate and 5-phosphoshikimic acid formed as an intermediate in the biosynthesis of aromatic amino acids and many other compounds.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

19 records
Show feature table
Start End DB Term Name
108 274 CDD cd01065 NAD_bind_Shikimate_DH
257 284 Pfam PF18317 Shikimate 5'-dehydrogenase C-terminal domain
257 284 InterPro IPR041121 SDH, C-terminal
11 284 NCBIfam TIGR00507 shikimate dehydrogenase
11 284 InterPro IPR011342 Shikimate dehydrogenase
3 280 PANTHER PTHR21089 SHIKIMATE DEHYDROGENASE
3 280 InterPro IPR022893 Shikimate dehydrogenase family
4 108 SUPERFAMILY SSF53223 Aminoacid dehydrogenase-like, N-terminal domain
4 108 InterPro IPR046346 Aminoacid dehydrogenase-like, N-terminal domain superfamily
13 120 FunFam G3DSA:3.40.50.10860:FF:000004 Quinate/shikimate dehydrogenase
9 287 Hamap MF_00222 Shikimate dehydrogenase (NADP(+)) [aroE].
9 287 InterPro IPR022893 Shikimate dehydrogenase family
13 275 Gene3D G3DSA:3.40.50.10860 Leucine Dehydrogenase, chain A, domain 1
110 260 Gene3D G3DSA:3.40.50.720 -
109 286 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains
109 286 InterPro IPR036291 NAD(P)-binding domain superfamily
14 96 Pfam PF08501 Shikimate dehydrogenase substrate binding domain
14 96 InterPro IPR013708 Shikimate dehydrogenase substrate binding, N-terminal
109 258 FunFam G3DSA:3.40.50.720:FF:000086 Quinate/shikimate 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
0.89
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Surrounding area
Pocket 2 P2Rank #2
0.173
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Surrounding area
Pocket 3 P2Rank #3
0.012
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Surrounding area
Pocket 4 P2Rank #4
0.007
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #6
0.312 Unusual size
Show in viewer
Surrounding area
Residue sets
UniProt: Active site:73-73 Proton acceptor
UniProt: Binding site:109-109
UniProt: Binding site:133-137
UniProt: Binding site:22-24
UniProt: Binding site:234-234
UniProt: Binding site:236-236
UniProt: Binding site:257-257
UniProt: Binding site:264-264
UniProt: Binding site:69-69
UniProt: Binding site:94-94
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_A0A0H3GJ74
AlphaFold DB — — full sequence — Viewing
ColabFold VK055_2498
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
ATR PDB via homolog 507.2 Da · LogP -1.63 · TPSA 279.1 Open detail RCSB PDB
DHK PDB via homolog Detail RCSB PDB
QIC PDB via homolog Detail RCSB PDB
SKM PDB via homolog Detail RCSB PDB
TLA 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
ATR RCSB PDB
2HK9
O67049 507.2 Da LogP -1.63 TPSA 279.1 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
DHK RCSB PDB
2O7Q
Q9SQT8 174.2 Da LogP -0.75 TPSA 98.0 ✓ Ro5 ✓ Clean C1[C@@H](C=C([C@H]([C@@H]1O)O)O)C(=O)O
QIC RCSB PDB
6BMQ
Q9SQT8 192.2 Da LogP -2.32 TPSA 118.2 ✓ Ro5 ✓ Clean C1[C@H](C([C@@H](CC1(C(=O)O)O)O)O)O
SKM RCSB PDB
2HK9
O67049 174.2 Da LogP -1.52 TPSA 98.0 ✓ Ro5 ✓ Clean C1[C@H]([C@@H]([C@@H](C=C1C(=O)O)O)O)O
TLA RCSB PDB
2GPT
Q9SQT8 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.

Sequence

UniProt A0A0H3GJ74

Pathways

BioCyc QUINATE-5-DEHYDROGENASE-RXN-QUINATE/NADP//DEHYDROQUINATE/NADPH/PROTON.42. BioCyc RXN-11174-SHIKIMATE/NAD//3-DEHYDRO-SHIKIMATE/NADH/PROTON.47. BioCyc QUINATE-5-DEHYDROGENASE-RXN-QUINATE/NAD//DEHYDROQUINATE/NADH/PROTON.40. KEGG R02413 BioCyc SHIKIMATE-5-DEHYDROGENASE-RXN