KpATCC43816 Protein target profile

ATP-dependent helicase HrpB

Accession: VK055_2420

Gene: AIK81017.1 hrpB 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3GJI5
Length 809
Pocket druggability (P2Rank · AlphaFold DB model) 0.596
Direct ligand evidence 0 54 total records
Functional annotation 0 EC 4 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 (%)
40.833 Lower values reduce human off-target concern.
Human E-value
5.56e-19
Gut microbiome similarity
2.3% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
N
DEG identity (%)
37.671 Higher values support similarity to known essential genes.

Structure confidence

ColabFold pLDDT
92.55 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) 0.596
Structure A0A0H3GJI5
Pocket Pocket 1
Druggability (FPocket) 0.159
Structure A0A0H3GJI5
Pocket Pocket 9
ColabFold model
P2Rank 0.546 · Pocket 1
FPocket 0.889 · Pocket 23
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 111 / 4744 genomes with a hit
Prevalence 2.3%

Metabolic context

Reactions catalyzed, pathway membership, and centrality in the genome-scale metabolic network.

This protein is not associated with the imported metabolic network for this genome.

Browse the genome's metabolic network

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MSSLPVAAVLPELLSALQHAPQVLLNAPTGAGKSTWLPLQILAEGNIAGRIILLEPRRLAARNVAQRLAELLGEKPGETVGFRMRAETCVGPQTRLEVVTEGILTRMIQRDPELTGVGLVILDEFHERSLQADLALALLLDVQQGLRDDLKLLIMSATLDNDRLQRLLPEAPVVVSEGRAYPVERRFSPLSAHQRFDEAVAVAVAELLRHEQGSMLLFLPGVGEIQRVLEQLTERVAEDVILCPLYGALPLSEQRKAILPAPAGKRKVVLATNIAETSLTIEGIRLVVDSAQERVARFDPRTGLTRLVTQRISQASMMQRAGRAGRLSPGICLHLLGKEQAERAAAQSEPEILHSDLSALLLELLQWGCHDPAALAWLDQPPAVNLAAARRLLEALSALDGERLSAFGRKMAALGNEPRLAAMLAAAQTDDEAVTAAKLAAILEEPPRGGLVDLGAVFSRQQANWQQRSQQLMKRLARRGGQPDAGLMAGLLASAFADRIARRRGQEGRYQLANGMGAMLDADDALGRHEWLIAPLLLQGSASPDARMLLALPVEIGELIAARPELAKSSDTVEWDEAQGTLKAWRRTVIGQLVIKTQPLAKPSEAELHQAMLNGIREKGLGVLNWTPEAEQLRLRLHCAAQWLPEEAWPAVDDASLLASLETWLLPQMNGVHSLRALKALDLRQALQDWLPWPLRQKLDRELPTHYTVPTGSRLAIRYHAENPPALAVRMQEMFGEATTPVIAEGRVPLVLELLSPAQRPLQITRDLSAFWQGSYREVQKEMKGRYPKHVWPDDPANAAPTRRSKKYS

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 GO

Subcellular localization

Localization
CytoplasmicMembrane

Gene Ontology (GO)

4
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0003676 Binding to a nucleic acid.
  • GO:0004386 Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive the unwinding of a DNA or RNA helix.
  • GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

34 records
Show feature table
Start End DB Term Name
226 328 SMART SM00490 helicmild6
226 328 InterPro IPR001650 Helicase, C-terminal
195 368 ProSiteProfiles PS51194 Superfamilies 1 and 2 helicase C-terminal domain profile.
195 368 InterPro IPR001650 Helicase, C-terminal
388 491 SMART SM00847 ha2_5
388 491 InterPro IPR007502 Helicase-associated domain
370 479 Gene3D G3DSA:1.20.120.1080 -
389 444 Pfam PF04408 Helicase associated domain (HA2)
389 444 InterPro IPR007502 Helicase-associated domain
1 179 Gene3D G3DSA:3.40.50.300 -
1 179 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
1 179 FunFam G3DSA:3.40.50.300:FF:002125 ATP-dependent helicase HrpB
14 177 ProSiteProfiles PS51192 Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile.
14 177 InterPro IPR014001 Helicase superfamily 1/2, ATP-binding domain
19 164 Pfam PF00270 DEAD/DEAH box helicase
19 164 InterPro IPR011545 DEAD/DEAH box helicase domain
4 808 NCBIfam TIGR01970 ATP-dependent helicase HrpB
4 808 InterPro IPR010225 ATP-dependent helicase HrpB
181 335 CDD cd18791 SF2_C_RHA
1 809 PIRSF PIRSF005496 ATP_hel_HrpB
1 809 InterPro IPR010225 ATP-dependent helicase HrpB
204 327 Pfam PF00271 Helicase conserved C-terminal domain
204 327 InterPro IPR001650 Helicase, C-terminal
180 347 Gene3D G3DSA:3.40.50.300 -
180 347 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
2 808 PANTHER PTHR43519 ATP-DEPENDENT RNA HELICASE HRPB
17 338 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
17 338 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
2 186 SMART SM00487 ultradead3
2 186 InterPro IPR014001 Helicase superfamily 1/2, ATP-binding domain
664 796 Pfam PF08482 ATP-dependent helicase C-terminal
664 796 InterPro IPR013689 ATP-dependent RNA helicase HrpB, C-terminal
787 809 MobiDBLite mobidb-lite consensus disorder prediction
4 176 CDD cd17990 DEXHc_HrpB

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
0.596
Show in viewer
Surrounding area
Pocket 2 P2Rank #2
0.53
Show in viewer
Surrounding area
Pocket 3 P2Rank #3
0.103
Show in viewer
Surrounding area
Pocket 4 P2Rank #4
0.049
Show in viewer
Surrounding area
Pocket 5 P2Rank #5
0.031
Show in viewer
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_A0A0H3GJI5
AlphaFold DB full sequence Viewing
ColabFold VK055_2420
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
ALF PDB via homolog 103.0 Da · LogP 1.30 · TPSA 0.0 Open detail RCSB PDB
ANP PDB via homolog Detail RCSB PDB
BEF PDB via homolog Detail RCSB PDB
CAC PDB via homolog Detail RCSB PDB
ZINC12360002 ZINC proposed compound · Tanimoto 0.810 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
ALF RCSB PDB P37024 103.0 Da LogP 1.30 TPSA 0.0 ✓ Ro5 ✓ Clean F[Al-](F)(F)F
ANP RCSB PDB P53131 506.2 Da LogP -2.06 TPSA 281.9 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
BEF RCSB PDB G0RY84 66.0 Da LogP 0.88 TPSA 0.0 ✓ Ro5 ✓ Clean [Be-](F)(F)F
CAC RCSB PDB G0RY84 137.0 Da LogP -0.52 TPSA 40.1 ✓ Ro5 ✓ Clean C[As](=O)(C)[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.