Protein target profile

KP13_02102

Delta-aminolevulinic acid dehydratase

Genome: KpKP13 Gene: AHE46102.1 hemB 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GNW5
Length 324
Pocket druggability 0.454
Direct ligand evidence 0 58 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.

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 (%)
42.384 Lower values reduce human off-target concern.
Human E-value
3.93e-76
Gut microbiome similarity
8.7% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
96.57 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

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 0.454
Structure A0A0H3GNW5
Pocket Pocket 1
P2Rank 0.587
Structure A0A0H3GNW5
Pocket Pocket 1
ColabFold model
FPocket 0.163 · Pocket 4
P2Rank 0.372 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 413 / 4744 genomes with a hit
Prevalence 8.7%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MTDLITRPRRLRQSAALRALFEETTLSLNDLVLPIFVEEEIDDYKAIEAMPGVMRIPEKYLAREIERIANAGIRSVMTFGISHHTDATGSDTWNENGLVARMSRICKSTVPEMIVMSDTCFCEYTSHGHCGVLCDHGVDNDATLENLGKQAVVAAAAGADFIAPSAAMDGQVQAIRRSLDAAGFTNTAIMSYSTKFASSFYGPFREAAGTALKGDRKTYQMSPMNRREAIRESLLDEAQGADCLMVKPAGAYLDILRDIRERSDLPLGAYQVSGEYAMIKFAAQAGAIDEEKVVLESLGAIKRAGADLIFSYFALDLAEKKILR

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

6
  • GO:0033014 The chemical reactions and pathways leading to the formation of tetrapyrroles, natural pigments containing four pyrrole rings joined by one-carbon units linking position 2 of one pyrrole ring to position 5 of the next.
  • GO:0004655 Catalysis of the reaction: 2 5-aminolevulinate = 2 H2O + H+ + porphobilinogen.
  • GO:0046872 Binding to a metal ion.
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0008270 Binding to a zinc ion (Zn).
  • GO:0006782 The chemical reactions and pathways resulting in the formation of protoporphyrinogen IX.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

27 records
Show feature table
Start End DB Term Name
1 323 PIRSF PIRSF001415 Porphbilin_synth
1 323 InterPro IPR001731 Delta-aminolevulinic acid dehydratase
4 319 SUPERFAMILY SSF51569 Aldolase
2 323 FunFam G3DSA:3.20.20.70:FF:000019 Delta-aminolevulinic acid dehydratase
240 252 ProSitePatterns PS00169 Delta-aminolevulinic acid dehydratase active site.
240 252 InterPro IPR030656 Delta-aminolevulinic acid dehydratase, active site
265 280 PRINTS PR00144 Delta-aminolevulinic acid dehydratase signature
265 280 InterPro IPR001731 Delta-aminolevulinic acid dehydratase
151 170 PRINTS PR00144 Delta-aminolevulinic acid dehydratase signature
151 170 InterPro IPR001731 Delta-aminolevulinic acid dehydratase
295 314 PRINTS PR00144 Delta-aminolevulinic acid dehydratase signature
295 314 InterPro IPR001731 Delta-aminolevulinic acid dehydratase
240 256 PRINTS PR00144 Delta-aminolevulinic acid dehydratase signature
240 256 InterPro IPR001731 Delta-aminolevulinic acid dehydratase
189 208 PRINTS PR00144 Delta-aminolevulinic acid dehydratase signature
189 208 InterPro IPR001731 Delta-aminolevulinic acid dehydratase
121 135 PRINTS PR00144 Delta-aminolevulinic acid dehydratase signature
121 135 InterPro IPR001731 Delta-aminolevulinic acid dehydratase
6 319 Pfam PF00490 Delta-aminolevulinic acid dehydratase
6 319 InterPro IPR001731 Delta-aminolevulinic acid dehydratase
3 321 SMART SM01004 ALAD_2
3 321 InterPro IPR001731 Delta-aminolevulinic acid dehydratase
9 320 CDD cd00384 ALAD_PBGS
2 324 Gene3D G3DSA:3.20.20.70 Aldolase class I
2 324 InterPro IPR013785 Aldolase-type TIM barrel
4 319 PANTHER PTHR11458 DELTA-AMINOLEVULINIC ACID DEHYDRATASE
4 319 InterPro IPR001731 Delta-aminolevulinic acid dehydratase

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
0.454
Likely same site as P2Rank 1 1.9 Å 11 shared residues 100% of smaller site
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Surrounding area
Site 2 FPocket #18
0.219
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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
0.587
Likely same site as FPocket 1 1.9 Å 11 shared residues 100% of smaller site
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Surrounding area
Site 2 P2Rank #2
0.264
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Surrounding area
Site 3 P2Rank #3
0.158
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Surrounding area
Site 4 P2Rank #4
0.042
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Surrounding area
Site 5 P2Rank #5
0.012
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Surrounding area
Residue sets
UniProt: Active site:195-195 Schiff-base intermediate with substrate
UniProt: Active site:247-247 Schiff-base intermediate with substrate
UniProt: Binding site:120-120
UniProt: Binding site:122-122
UniProt: Binding site:130-130
UniProt: Binding site:205-205
UniProt: Binding site:216-216
UniProt: Binding site:232-232
UniProt: Binding site:273-273
UniProt: Binding site:312-312
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_A0A0H3GNW5
AlphaFold DB full sequence Viewing
ColabFold KP13_02102
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.

58 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 8 records from similar proteins
Structural ligands 7 0 loaded crystals
Measured bioactivity 1 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
4OX PDB via homolog 216.2 Da · LogP 1.46 · TPSA 91.7 Open detail RCSB PDB
AYC PDB via homolog Detail RCSB PDB
DSB PDB via homolog Detail RCSB PDB
LAF PDB via homolog Detail RCSB PDB
PBG 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
4OX RCSB PDB P0ACB2 216.2 Da LogP 1.46 TPSA 91.7 ✓ Ro5 ✓ Clean C(CCC(=O)CCC(=O)O)CCC(=O)O
AYC RCSB PDB Q59643 187.2 Da LogP -0.06 TPSA 83.5 ✓ Ro5 ✓ Clean C[C@H](C(=O)CCC(=O)O)NC(=O)C
DSB RCSB PDB P0ACB2 230.2 Da LogP 0.63 TPSA 108.7 ✓ Ro5 ✓ Clean C(CC(=O)CCC(=O)O)C(=O)CCC(=O)O
LAF RCSB PDB Q59643 134.1 Da LogP 0.39 TPSA 54.4 ✓ Ro5 ✓ Clean C(CC(=O)O)C(=O)CF
PBG RCSB PDB P0ACB2 226.2 Da LogP 0.12 TPSA 116.4 ✓ Ro5 ✓ Clean c1c(c(c([nH]1)CN)CC(=O)O)CCC(=O)O
PE5 RCSB PDB Q59643 398.5 Da LogP 0.13 TPSA 94.1 ✓ Ro5 ✓ Clean CCOCCOCCOCCOCCOCCOCCOCCOCCO
SHF RCSB PDB P0ACB2 116.1 Da LogP 0.44 TPSA 54.4 ✓ Ro5 ✓ Clean CC(=O)CCC(=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.