KpKP13 Protein target profile

Bifunctional aspartokinase/homoserine dehydrogenase 1

Accession: KP13_01993

Gene: thrA AHE46431.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GHZ9
Length 818
Pocket druggability (P2Rank · AlphaFold DB model) 0.763
Direct ligand evidence 0 55 total records
Functional annotation 0 EC 13 GO
Target summary

Strong target candidate with converging metabolic, structural and chemical evidence.

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
No hit
Gut microbiome similarity
3.3% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Structure confidence

ColabFold pLDDT
92.14 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) 0.763
Structure A0A0H3GHZ9
Pocket Pocket 1
Druggability (FPocket) 0.729
Structure A0A0H3GHZ9
Pocket Pocket 54
ColabFold model
P2Rank 0.742 · Pocket 1
FPocket 0.589 · Pocket 19
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 155 / 4744 genomes with a hit
Prevalence 3.3%

Sequence

Primary amino-acid sequence viewer.

MLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTIGGQDALPNIADAERIFAELLQGLADAQPAFPLAQLKAFVEQEFAQIKHVLHGISLLGQCPDSVNAALICRGEKLSIAIMAGLLEARGHKVSVINPVEKLLAVGHYLESTVDIAESTRRIAASQIPADHMILMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQVPDARLLKSMSYQEAMELSYFGAKVLHPRTIAPIAQFQIPCLIKNTGNPQAPGTLIGASRDEDDLPVKGISNLNNMAMFNVSGPGMKGMVGMAARVFATMSRAGISVVLITQSSSEYSISFCVPQSDCARAKRAMEDEFYLELKEGLLEPLAIMERLAIISVVGDGMRTLRGISAKFFAALARANINIVAIAQGSSERSISVVVSNDDATTGVRVTHQMLFNTDQVIEVFVIGVGGVGGALLEQIKRQQGWLKNKHIDLRVCGVANSQALLTSVHGLNLENWSAELAEAKEPFNLGRLIRLVKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSLDYYHQLRHAASSSRRKFLYDTNVGAGLPVIENLQNLLNAGDELRHFSGILSGSLSFIFGKLDEGVSFSAATAMAREMGYTEPDPRDDLSGVDVARKLLILARETGRELELADIIVESALPPDFDASGDVETFMARLPSLDDGFASRVAKARDEGKVLRYVGNIEEDGTCRVKIAAVDGNDPLFKVKNGENALAFYSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSWKLGV

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

13 GO

Subcellular localization

Localization
Cytoplasmic

Gene Ontology (GO)

13
  • GO:0009067 The chemical reactions and pathways resulting in the formation of amino acids of the aspartate family, comprising asparagine, aspartate, lysine, methionine and threonine.
  • GO:0006520 The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups.
  • GO:0004412 Catalysis of the reaction: L-homoserine + NADP+ = L-aspartate-4-semialdehyde + NADPH + H+.
  • 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:0004072 Catalysis of the reaction: L-aspartate + ATP = 4-phospho-L-aspartate + ADP + 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:0008652 The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0046872 Binding to a metal ion.
  • GO:0009090 The chemical reactions and pathways resulting in the formation of homoserine, alpha-amino-gamma-hydroxybutyric acid.
  • GO:0009089 OBSOLETE. The chemical reactions and pathways resulting in the formation of lysine, via the intermediate diaminopimelate.
  • GO:0009086 OBSOLETE. The chemical reactions and pathways resulting in the de novo formation of L-methionine (2-amino-4-(methylthio)butanoic acid), a sulfur-containing, essential amino acid found in peptide linkage in proteins.
  • GO:0009088 The chemical reactions and pathways resulting in the formation of L-threonine (2-amino-3-hydroxybutyric acid), a polar, uncharged, essential amino acid found in peptide linkage in proteins.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

48 records
Show feature table
Start End DB Term Name
2 293 Gene3D G3DSA:3.40.1160.10 -
2 293 InterPro IPR036393 Acetylglutamate kinase-like superfamily
392 451 Pfam PF13840 ACT domain
392 451 InterPro IPR027795 CASTOR, ACT domain
301 379 SUPERFAMILY SSF55021 ACT-like
301 379 InterPro IPR045865 ACT-like domain
464 810 Gene3D G3DSA:3.40.50.720 -
394 459 CDD cd04922 ACT_AKi-HSDH-ThrA_2
300 462 Gene3D G3DSA:3.30.2130.10 -
1 295 FunFam G3DSA:3.40.1160.10:FF:000022 Bifunctional aspartokinase/homoserine dehydrogenase
462 634 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains
462 634 InterPro IPR036291 NAD(P)-binding domain superfamily
2 814 PANTHER PTHR43070 -
2 814 InterPro IPR011147 Bifunctional aspartokinase/homoserine dehydrogenase
465 635 FunFam G3DSA:3.40.50.720:FF:000083 Bifunctional aspartokinase/homoserine dehydrogenase
1 816 PIRSF PIRSF000727 ThrA
1 816 InterPro IPR011147 Bifunctional aspartokinase/homoserine dehydrogenase
612 796 SUPERFAMILY SSF55347 Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
301 460 FunFam G3DSA:3.30.2130.10:FF:000001 Bifunctional aspartokinase/homoserine dehydrogenase
2 458 NCBIfam TIGR00657 aspartate kinase
2 458 InterPro IPR001341 Aspartate kinase
623 793 FunFam G3DSA:3.30.360.10:FF:000006 Bifunctional aspartokinase/homoserine dehydrogenase
381 474 SUPERFAMILY SSF55021 ACT-like
381 474 InterPro IPR045865 ACT-like domain
658 680 ProSitePatterns PS01042 Homoserine dehydrogenase signature.
658 680 InterPro IPR019811 Homoserine dehydrogenase, conserved site
470 603 Pfam PF03447 Homoserine dehydrogenase, NAD binding domain
470 603 InterPro IPR005106 Aspartate/homoserine dehydrogenase, NAD-binding
318 392 ProSiteProfiles PS51671 ACT domain profile.
318 392 InterPro IPR002912 ACT domain
2 294 CDD cd04257 AAK_AK-HSDH
2 294 InterPro IPR041743 Bifunctional aspartokinase/homoserine dehydrogenase, N-terminal catalytic domain
1 9 ProSitePatterns PS00324 Aspartokinase signature.
1 9 InterPro IPR018042 Aspartate kinase, conserved site
39 140 Gene3D G3DSA:1.20.120.1320 Aspartokinase, catalytic domain
39 140 InterPro IPR042199 Aspartokinase/Bifunctional aspartokinase/homoserine dehydrogenase, catalytic domain
623 793 Gene3D G3DSA:3.30.360.10 Dihydrodipicolinate Reductase; domain 2
322 374 Pfam PF01842 ACT domain
322 374 InterPro IPR002912 ACT domain
2 294 SUPERFAMILY SSF53633 Carbamate kinase-like
2 294 InterPro IPR036393 Acetylglutamate kinase-like superfamily
313 392 CDD cd04921 ACT_AKi-HSDH-ThrA-like_1
612 809 Pfam PF00742 Homoserine dehydrogenase
612 809 InterPro IPR001342 Homoserine dehydrogenase, catalytic
2 282 Pfam PF00696 Amino acid kinase family
2 282 InterPro IPR001048 Aspartate/glutamate/uridylate kinase
399 476 ProSiteProfiles PS51671 ACT domain profile.
399 476 InterPro IPR002912 ACT domain

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
0.763
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Surrounding area
Pocket 2 P2Rank #2
0.548
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Surrounding area
Pocket 3 P2Rank #3
0.247
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Surrounding area
Pocket 4 P2Rank #4
0.155
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Surrounding area
Pocket 5 P2Rank #5
0.139
Likely same site as FPocket 1 2.5 Å 15 shared residues 100% of smaller site
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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 #54
0.729
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Surrounding area
Pocket 2 FPocket #1
0.644 Unusual size
Likely same site as P2Rank 5 2.5 Å 15 shared residues 100% of smaller site
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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_A0A0H3GHZ9
AlphaFold DB full sequence Viewing
ColabFold KP13_01993
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
178 PDB via homolog 302.4 Da · LogP 5.50 · TPSA 40.5 Open detail RCSB PDB
HSE PDB via homolog Detail RCSB PDB
NDA PDB via homolog Detail RCSB PDB
NHO PDB via homolog Detail RCSB PDB
TAR 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
178 RCSB PDB P31116 302.4 Da LogP 5.50 TPSA 40.5 1 viol. ✓ Clean CC(C)c1cc(ccc1O)Sc2ccc(c(c2)C(C)C)O
HSE RCSB PDB P31116 119.1 Da LogP -1.22 TPSA 83.5 ✓ Ro5 ✓ Clean C(CO)[C@@H](C(=O)O)N
NDA RCSB PDB P31116 649.4 Da LogP -3.29 TPSA 304.0 3 viol. ✓ Clean c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P…
NHO RCSB PDB P31116 809.6 Da LogP -4.61 TPSA 418.9 3 viol. ✓ Clean c1c[n+](cc(c1[C@@H](C(=O)C[C@@H](C(=O)O)N)O)C(=…
TAR RCSB PDB Q9LYU8 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.