Protein target profile

KP13_03769

Histidinol-phosphate aminotransferase

Genome: KpKP13 Gene: hisC AHE43694.1 3D evidence: Experimental + ColabFold model UniProt A6TBC4
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Length 353
Pocket druggability 0.775
Direct ligand evidence 0 54 total records
Functional annotation 0 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

Independent pocket support: FPocket + P2Rank Both predictors report a high-scoring binding site (FPocket 0.78, P2Rank 0.81). Use the 3D pocket comparison to verify whether they identify the same site. Experimental structure available At least one PDB experimental structure is loaded, not just a predicted model - stronger structural coverage than AlphaFold/ColabFold alone. Strong predicted binding pocket FPocket selected-pocket score 0.78. This is a computational pocket signal, not binding validation. Second pocket predictor agrees P2Rank predicted binding-site probability 0.81. Review the complete evidence below

Risks to review

Human similarity Top human hit identity: 30.734%. This target also has a predicted binding pocket (FPocket 0.78) — check the ligand evidence before deprioritizing on off-target risk alone. Microbiome similarity 139 of 4744 screened genomes (2.9%) have a significant similarity hit. This target also has a predicted binding pocket (FPocket 0.78) — check the ligand evidence before deprioritizing on off-target risk alone. Mixed conservation Core/accessory calls are not fully concordant.

Evidence gaps

No metabolic context No SBML/network-derived reaction evidence is loaded for 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 (%)
30.734 Lower values reduce human off-target concern.
Human E-value
1.3e-08
Gut microbiome similarity
2.9% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
59.195 Higher values support similarity to known essential genes.
DEG E-value
5.989999999999999e-159 Smaller values mean stronger essential-gene similarity.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
97.3 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

PDB experimental structure

The selected pocket score is the FPocket value used for ranking after applying the curated structure priority. It estimates small-molecule pocket quality; it is not experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

FPocket 0.775
Structure 7SZP
Pocket Pocket 1
P2Rank 0.811
Structure 7SZP
Pocket Pocket 1
ColabFold model
FPocket 0.439 · Pocket 1
P2Rank 0.878 · Pocket 1
Core conservation Accessory gene
Roary core
CoreCruncher accessory
Gut microbiome 139 / 4744 genomes with a hit
Prevalence 2.9%

Cross-references

External database identifiers for this protein, its structures, ligands, and metabolic reactions.

Sequence

UniProt A6TBC4

Structure

PDB 7SZP

Sequence

Primary amino-acid sequence viewer.

MSIEDLARANVRALTPYQSARRLGGKGDVWLNANEFPTAVAFQLTEQTLNRYPEPQPKAVIESYARYAEVKPEQVLVSRGADEGIELLIRAFCEPGEDAVLYCPPTYGMYSVSAETIGVECRTVPTLTDWQLDLPGIEARLDGVKVVFVCSPNNPTGQIIDPQSMRDLLEMTRGKAIVVADEAYIEFCPQATLAGWLSDYPHLVVLRTLSKAFALAGLRCGFTLANAEVINVLLKVIAPYPLSTPVADIAAQALSPEGIAAMRQRVAQILDERRYLVEQLRGIACVEQVFDSETNYVLARITASSAVFKSLWDQGIILRDQNKQPSLSGCLRITIGTRAESQRVIDALTAENV

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

6 GO

Gene Ontology (GO)

6
  • GO:0030170 Binding to pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
  • GO:0004400 Catalysis of the reaction: L-histidinol-phosphate + 2-oxoglutarate = 3-(imidazol-4-yl)-2-oxopropyl phosphate + L-glutamate.
  • GO:0000105 The chemical reactions and pathways resulting in the formation of L-histidine, 2-amino-3-(1H-imidazol-4-yl)propanoic acid.
  • GO:0009058 A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
  • GO:0016740 Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
  • GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

17 records
Show feature table
Start End DB Term Name
8 349 NCBIfam TIGR01141 histidinol-phosphate transaminase
8 349 InterPro IPR005861 Histidinol-phosphate aminotransferase family
28 348 CDD cd00609 AAT_like
6 352 Hamap MF_01023 Histidinol-phosphate aminotransferase [hisC].
6 352 InterPro IPR005861 Histidinol-phosphate aminotransferase family
6 344 Gene3D G3DSA:3.90.1150.10 Aspartate Aminotransferase, domain 1
6 344 InterPro IPR015422 Pyridoxal phosphate-dependent transferase, small domain
208 217 ProSitePatterns PS00599 Aminotransferases class-II pyridoxal-phosphate attachment site.
208 217 InterPro IPR001917 Aminotransferase, class-II, pyridoxal-phosphate binding site
51 255 Gene3D G3DSA:3.40.640.10 -
51 255 InterPro IPR015421 Pyridoxal phosphate-dependent transferase, major domain
44 348 Pfam PF00155 Aminotransferase class I and II
44 348 InterPro IPR004839 Aminotransferase, class I/classII
5 349 SUPERFAMILY SSF53383 PLP-dependent transferases
5 349 InterPro IPR015424 Pyridoxal phosphate-dependent transferase
7 348 PANTHER PTHR42885 HISTIDINOL-PHOSPHATE AMINOTRANSFERASE-RELATED
51 255 FunFam G3DSA:3.40.640.10:FF:000032 Histidinol-phosphate aminotransferase

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 · FPocket

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

Site 1 FPocket #1
0.775
Likely same site as P2Rank 1 3.4 Å 15 shared residues 100% of smaller site
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Surrounding area

Binding pockets · P2Rank

Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Site 1 P2Rank #1
0.811
Likely same site as FPocket 1 3.4 Å 15 shared residues 100% of smaller site
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Surrounding area
Site 2 P2Rank #2
0.01
Show in viewer
Surrounding area
All structural evidence 1 experimental · 1 predicted

Structural evidence

1 + 1

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
PDB 7SZP
X-ray — A —
PDBe RCSB PDBj File
Viewing
ColabFold KP13_03769
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.

54 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 4 records from similar proteins
Structural ligands 4 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
144 PDB via homolog 122.1 Da · LogP -1.72 · TPSA 60.7 Open detail RCSB PDB
HSA PDB via homolog Detail RCSB PDB
PMP PDB via homolog Detail RCSB PDB
SIN PDB via homolog Detail RCSB PDB
ZINC1532708 ZINC proposed compound · Tanimoto 1.000 Detail ZINC

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
144 RCSB PDB
3CQ5
Q9KJU4 122.1 Da LogP -1.72 TPSA 60.7 ✓ Ro5 ✓ Clean C[N+](CO)(CO)CO
HSA RCSB PDB
1FG3
P06986 221.2 Da LogP -0.61 TPSA 121.5 ✓ Ro5 ✓ Clean c1c(nc[nH]1)CC(COP(=O)(O)O)N
PMP RCSB PDB
1FG7
P06986 248.2 Da LogP 0.16 TPSA 125.9 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CN)O
SIN RCSB PDB
4R5Z
P9WML5 118.1 Da LogP -0.06 TPSA 74.6 ✓ Ro5 ✓ Clean C(CC(=O)O)C(=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.