KpKP13 Protein target profile

Histidine biosynthesis bifunctional protein

Accession: KP13_03770

Gene: hisB AHE43693.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GV71
Length 355
Pocket druggability (P2Rank · AlphaFold DB model) 0.13
Direct ligand evidence 0 54 total records
Functional annotation 0 EC 6 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
No hit
Gut microbiome similarity
3.7% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
60.497 Higher values support similarity to known essential genes.
DEG E-value
5.1e-165 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
95.33 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) 0.13
Structure A0A0H3GV71
Pocket Pocket 1
Druggability (FPocket) 0.318
Structure A0A0H3GV71
Pocket Pocket 4
ColabFold model
P2Rank 0.231 · Pocket 1
FPocket 0.846 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 177 / 4744 genomes with a hit
Prevalence 3.7%

Sequence

Primary amino-acid sequence viewer.

MTQKYLFIDRDGTLISEPPEDFQVDRFDKLAFEPQVIPALLKLQQEGYKLVMITNQDGLGTDSLPQEAFDGPHNLMMQIFASQCVNFEEVLICPHFPGDNCACRKPKTQLVLPWLEEGVLDKSHSYVIGDRATDLELADNMGITGLRYDRETLDWPTICEQLTRRDRYAHVERVTKETQVDVKVWLDREGGSKIHTGVGFFDHMLDQIATHGGFRMEVNVGGDLYIDDHHTVEDTGLALGEALKLALGDKRGINRFGFVLPMDECLARCALDISGRPHLEYKADFTYQRVGDLSTEMVEHFFRSLSYTMAVTLHLKTKGKNDHHRVESLFKAFGRTLRQAIRVQGDALPSSKGVL

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

6 GO

Subcellular localization

Localization
Cytoplasmic

Gene Ontology (GO)

6
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0000105 The chemical reactions and pathways resulting in the formation of L-histidine, 2-amino-3-(1H-imidazol-4-yl)propanoic acid.
  • GO:0004424 Catalysis of the reaction: D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate = 3-(imidazol-4-yl)-2-oxopropyl phosphate + H2O.
  • GO:0016791 Catalysis of the hydrolysis of a phosphoric monoester, releasing a phosphate.
  • GO:0004401 Catalysis of the reaction: L-histidinol phosphate + H2O = L-histidinol + phosphate.
  • GO:0046872 Binding to a metal ion.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

37 records
Show feature table
Start End DB Term Name
160 355 PANTHER PTHR23133 IMIDAZOLEGLYCEROL-PHOSPHATE DEHYDRATASE HIS7
160 355 InterPro IPR000807 Imidazoleglycerol-phosphate dehydratase
4 147 NCBIfam TIGR01662 HAD-IIIA family hydrolase
4 147 InterPro IPR006549 HAD-superfamily hydrolase,subfamily IIIA
226 239 ProSitePatterns PS00954 Imidazoleglycerol-phosphate dehydratase signature 1.
226 239 InterPro IPR020565 Imidazoleglycerol-phosphate dehydratase, conserved site
5 144 NCBIfam TIGR01656 histidinol-phosphate phosphatase domain
5 144 InterPro IPR006543 Histidinol-phosphate phosphatase
319 331 ProSitePatterns PS00955 Imidazoleglycerol-phosphate dehydratase signature 2.
319 331 InterPro IPR020565 Imidazoleglycerol-phosphate dehydratase, conserved site
162 254 Gene3D G3DSA:3.30.230.40 Imidazole glycerol phosphate dehydratase; domain 1
162 254 InterPro IPR038494 Imidazole glycerol phosphate dehydratase domain superfamily
1 162 FunFam G3DSA:3.40.50.1000:FF:000061 Histidine biosynthesis bifunctional protein HisB
167 355 Hamap MF_00076 Imidazoleglycerol-phosphate dehydratase [hisB].
167 355 InterPro IPR000807 Imidazoleglycerol-phosphate dehydratase
1 161 Gene3D G3DSA:3.40.50.1000 -
1 161 InterPro IPR023214 HAD superfamily
2 355 Hamap MF_01022 Histidine biosynthesis bifunctional protein HisB [hisB].
2 355 InterPro IPR020566 Histidine biosynthesis bifunctional protein HisB
103 145 Pfam PF13242 HAD-hyrolase-like
4 148 CDD cd07503 HAD_HisB-N
167 251 SUPERFAMILY SSF54211 Ribosomal protein S5 domain 2-like
167 251 InterPro IPR020568 Ribosomal protein S5 domain 2-type fold
255 355 Gene3D G3DSA:3.30.230.40 Imidazole glycerol phosphate dehydratase; domain 1
255 355 InterPro IPR038494 Imidazole glycerol phosphate dehydratase domain superfamily
3 162 NCBIfam TIGR01261 HisB N-terminal histidinol-phosphatase domain
3 162 InterPro IPR005954 Histidine biosynthesis bifunctional protein, N-terminal histidinol-phosphatase domain
255 355 FunFam G3DSA:3.30.230.40:FF:000001 Imidazoleglycerol-phosphate dehydratase HisB
169 355 CDD cd07914 IGPD
169 355 InterPro IPR000807 Imidazoleglycerol-phosphate dehydratase
196 337 Pfam PF00475 Imidazoleglycerol-phosphate dehydratase
196 337 InterPro IPR000807 Imidazoleglycerol-phosphate dehydratase
160 254 FunFam G3DSA:3.30.230.40:FF:000003 Imidazoleglycerol-phosphate dehydratase HisB
1 156 SUPERFAMILY SSF56784 HAD-like
1 156 InterPro IPR036412 HAD-like superfamily
252 342 SUPERFAMILY SSF54211 Ribosomal protein S5 domain 2-like
252 342 InterPro IPR020568 Ribosomal protein S5 domain 2-type fold

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
0.13
Show in viewer
Surrounding area
Pocket 2 P2Rank #2
0.009
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #4
0.318
Show in viewer
Surrounding area
Residue sets
UniProt: Active site:11-11 Proton donor
UniProt: Active site:9-9 Nucleophile
UniProt: Binding site:101-101
UniProt: Binding site:103-103
UniProt: Binding site:11-11
UniProt: Binding site:130-130
UniProt: Binding site:9-9
UniProt: Binding site:93-93
UniProt: Binding site:95-95
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_A0A0H3GV71
AlphaFold DB full sequence Viewing
ColabFold KP13_03770
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 and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 20 records from similar proteins
Structural ligands 5 0 loaded crystals
Measured bioactivity 15 direct and transferred ChEMBL records
Proposed compounds 34 similarity-based ZINC candidates
Best available ligand signal
5DL PDB via homolog 207.1 Da · LogP -1.18 · TPSA 108.5 Open detail RCSB PDB
5LD PDB via homolog Detail RCSB PDB
EMC PDB via homolog Detail RCSB PDB
IYP PDB via homolog Detail RCSB PDB
TRI 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
5DL RCSB PDB O23346 207.1 Da LogP -1.18 TPSA 108.5 ✓ Ro5 ✓ Clean c1ncn(n1)C[C@@H](CP(=O)(O)O)O
5LD RCSB PDB L8H477 207.1 Da LogP -1.18 TPSA 108.5 ✓ Ro5 ✓ Clean c1ncn(n1)C[C@H](CP(=O)(O)O)O
EMC RCSB PDB P0CO22 229.7 Da LogP 0.97 TPSA 0.0 ✓ Ro5 ✓ Clean CC[Hg+]
IYP RCSB PDB O23346 238.1 Da LogP -1.09 TPSA 135.9 ✓ Ro5 ✓ Clean c1c([nH]cn1)[C@@H]([C@@H](COP(=O)(O)O)O)O
TRI RCSB PDB O23346 69.1 Da LogP -0.20 TPSA 41.6 ✓ Ro5 ✓ Clean c1[nH]cnn1

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.