KpKP13 Protein target profile

NADP-specific glutamate dehydrogenase

Accession: KP13_05411

Gene: AHE45055.1 gdhA 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GN61
Length 447
Pocket druggability (P2Rank · AlphaFold DB model) 0.889
Direct ligand evidence 0 57 total records
Functional annotation 0 EC 7 GO
Target summary

Target candidate with partial support; inspect missing evidence before prioritizing.

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 (%)
31.771 Lower values reduce human off-target concern.
Human E-value
4.71e-17
Gut microbiome similarity
67.8% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
55.251 Higher values support similarity to known essential genes.
DEG E-value
0.0 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
96.44 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) 0.889
Structure A0A0H3GN61
Pocket Pocket 1
Druggability (FPocket) 0.361
Structure A0A0H3GN61
Pocket Pocket 14
ColabFold model
P2Rank 0.846 · Pocket 1
FPocket 0.285 · Pocket 24
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 3218 / 4744 genomes with a hit
Prevalence 67.8%

Sequence

Primary amino-acid sequence viewer.

MDQTCTLEGFLTRVQQRDPHQTEFAQAVREVMTTLWPFLEENPRYRQLALLERLVEPERVIQFRVVWVDDRNQVQVNRAWRVQFNSAIGPYKGGMRFHPSVNLSILKFLGFEQTFKNALTTLPMGGGKGGSDFDPKGKSDGEVMRFCQALMTELYRHLGPDTDVPAGDIGVGGREVGFMAGMMRKLSNNSACVFTGKGLSFGGSLIRPEATGYGLIYFTEAMLKRHGLGFEGARVAVSGSGNVAQYAIEKAMELGARVVTASDSNGTVVDEAGFTKEKLARLIDIKERAHGRVADYAREFGLTYLEGQQPWSVPVDIALPCATQNELDVDAARQLIANGVKAVAEGANMPTTIAATDLFLEAGVLFAPGKAANAGGVATSGLEMAQNAARMGWKAEKVDARLHHIMLDIHHACVQYGGEAKQTNYVRGANIAGFVKVADAMLAQGVI

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

7 GO

Subcellular localization

Localization
Unknown

Gene Ontology (GO)

7
  • 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:0006520 The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups.
  • GO:0016639 Catalysis of an oxidation-reduction (redox) reaction in which a CH-NH2 group acts as a hydrogen or electron donor and reduces NAD+ or NADP.
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0004354 Catalysis of the reaction: L-glutamate + NADP+ + H2O = 2-oxoglutarate + NH4+ + NADPH + H+.
  • 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.
  • GO:0006537 OBSOLETE. The chemical reactions and pathways resulting in the formation of glutamate, the anion of 2-aminopentanedioic acid.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

32 records
Show feature table
Start End DB Term Name
22 447 PIRSF PIRSF000185 Glu_DH
22 447 InterPro IPR014362 Glutamate dehydrogenase
7 196 SUPERFAMILY SSF53223 Aminoacid dehydrogenase-like, N-terminal domain
7 196 InterPro IPR046346 Aminoacid dehydrogenase-like, N-terminal domain superfamily
195 446 CDD cd05313 NAD_bind_2_Glu_DH
195 446 InterPro IPR033922 NAD(P) binding domain of glutamate dehydrogenase
383 447 Gene3D G3DSA:1.10.285.10 Glutamate Dehydrogenase, chain A, domain 3
6 446 PANTHER PTHR43571 NADP-SPECIFIC GLUTAMATE DEHYDROGENASE 1-RELATED
209 374 FunFam G3DSA:3.40.50.720:FF:000030 Glutamate dehydrogenase
204 445 SMART SM00839 ELFV_dehydrog_3
204 445 InterPro IPR006096 Glutamate/phenylalanine/leucine/valine/L-tryptophan dehydrogenase, C-terminal
57 184 Pfam PF02812 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain
57 184 InterPro IPR006097 Glutamate/phenylalanine/leucine/valine/L-tryptophan dehydrogenase, dimerisation domain
55 190 FunFam G3DSA:3.40.50.10860:FF:000002 Glutamate dehydrogenase
122 135 ProSitePatterns PS00074 Glu / Leu / Phe / Val dehydrogenases active site.
122 135 InterPro IPR033524 Leu/Phe/Val dehydrogenases active site
55 190 Gene3D G3DSA:3.40.50.10860 Leucine Dehydrogenase, chain A, domain 1
10 382 Gene3D G3DSA:1.10.285.10 Glutamate Dehydrogenase, chain A, domain 3
379 447 FunFam G3DSA:1.10.285.10:FF:000001 Glutamate dehydrogenase
202 445 Pfam PF00208 Glutamate/Leucine/Phenylalanine/Valine dehydrogenase
202 445 InterPro IPR006096 Glutamate/phenylalanine/leucine/valine/L-tryptophan dehydrogenase, C-terminal
202 446 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains
202 446 InterPro IPR036291 NAD(P)-binding domain superfamily
209 373 Gene3D G3DSA:3.40.50.720 -
235 255 PRINTS PR00082 Glutamate/leucine/phenylalanine/valine dehydrogenase signature
235 255 InterPro IPR006095 Glutamate/phenylalanine/leucine/valine/L-tryptophan dehydrogenase
114 128 PRINTS PR00082 Glutamate/leucine/phenylalanine/valine dehydrogenase signature
114 128 InterPro IPR006095 Glutamate/phenylalanine/leucine/valine/L-tryptophan dehydrogenase
372 383 PRINTS PR00082 Glutamate/leucine/phenylalanine/valine dehydrogenase signature
372 383 InterPro IPR006095 Glutamate/phenylalanine/leucine/valine/L-tryptophan dehydrogenase
193 215 PRINTS PR00082 Glutamate/leucine/phenylalanine/valine dehydrogenase signature
193 215 InterPro IPR006095 Glutamate/phenylalanine/leucine/valine/L-tryptophan 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
0.889
Likely same site as FPocket 14 6.5 Å 27 shared residues 96% of smaller site
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Surrounding area
Pocket 2 P2Rank #2
0.437
Likely same site as FPocket 14 6.9 Å 18 shared residues 100% of smaller site
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Surrounding area
Pocket 3 P2Rank #3
0.012
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Surrounding area
Pocket 4 P2Rank #4
0.006
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Surrounding area
Pocket 5 P2Rank #5
0.005
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Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #14
0.361 Unusual size
Likely same site as P2Rank 1 6.5 Å 27 shared residues 96% of smaller site
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Surrounding area
Pocket 2 FPocket #22
0.33
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Surrounding area
Residue sets
UniProt: Active site:128-128 Proton donor
UniProt: Binding site:113-113
UniProt: Binding site:116-116
UniProt: Binding site:167-167
UniProt: Binding site:211-211
UniProt: Binding site:242-242
UniProt: Binding site:380-380
UniProt: Binding site:92-92
UniProt: Site:168-168 Important 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_A0A0H3GN61
AlphaFold DB full sequence Viewing
ColabFold KP13_05411
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
8G0 PDB via homolog 166.1 Da · LogP 1.08 · TPSA 74.6 Open detail RCSB PDB
A2R PDB via homolog Detail RCSB PDB
AKG PDB via homolog Detail RCSB PDB
MLI PDB via homolog Detail RCSB PDB
NH4 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
8G0 RCSB PDB B6V7E4 166.1 Da LogP 1.08 TPSA 74.6 ✓ Ro5 ✓ Clean c1cc(cc(c1)C(=O)O)C(=O)O
A2R RCSB PDB T2D1F5 639.3 Da LogP -3.17 TPSA 338.0 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
AKG RCSB PDB B6V7E4 146.1 Da LogP -0.50 TPSA 91.7 ✓ Ro5 ✓ Clean C(CC(=O)O)C(=O)C(=O)O
MLI RCSB PDB T2D1F5 102.0 Da LogP -3.12 TPSA 80.3 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(=O)[O-]
NH4 RCSB PDB Q72IC1 18.0 Da LogP 0.38 TPSA 36.5 ✓ Ro5 ✓ Clean [NH4+]
SIN RCSB PDB T2D1F5 118.1 Da LogP -0.06 TPSA 74.6 ✓ Ro5 ✓ Clean C(CC(=O)O)C(=O)O
TLA RCSB PDB T2D1F5 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.