KpATCC43816 Protein target profile

DEAD/DEAH box helicase family protein

Accession: VK055_2516

Gene: AIK81113.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3GRL2
Length 968
Pocket druggability (P2Rank · AlphaFold DB model) 0.937
Direct ligand evidence 0 55 total records
Functional annotation 0 EC 4 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 (%)
28.492 Lower values reduce human off-target concern.
Human E-value
2.13e-07
Gut microbiome similarity
3.1% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Structure confidence

ColabFold pLDDT
89.65 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) 0.937
Structure A0A0H3GRL2
Pocket Pocket 1
Druggability (FPocket) 0.891
Structure A0A0H3GRL2
Pocket Pocket 1
ColabFold model
P2Rank 0.933 · Pocket 1
FPocket 0.458 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 149 / 4744 genomes with a hit
Prevalence 3.1%

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.

MPFTLGQRWISDTESELGLGTVVALDARMVTLLFPAIGENRLYSRNDSPITRVMFNPGDTITSHEGWQLHVDKVNEENGLLSYTGTRLDTQETNVTLREVLLDSKLVFSKPQDRLFAGQIDRMDRFALRYRARKFQSEQYRMPWSGLRGQRTSLIPHQLHIAHDVGRRHAPRVLLADEVGLGKTIEAGMILHQQLLSGAAERVLIVVPETLQHQWLVEMLRRFNLRFSLFDDERYAEAQHDAYNPFETEQLVICSLDFVRRSKQRLEHLCDAEWDLMVVDEAHHLVWSEEAPSREYQAIEQLAERVPGILLLTATPEQLGMESHFARLRLLDPNRFHDFEQFVEEQQNYRPVADAVALLLAGNKLSDSELNTLGDLIGEQDIEPLLQAANSDREDAQAARQELISMLMDRHGTSRVLFRNTRNGVKGFPKRELHTIRLPLPTQYQTAIKVSGIMGARKTAEERARDMLYPEQIYQEFEGDTGTWWNFDPRVEWLMGYLTSHRSQKVLVICAKAATALQLEQVLREREGIRAAVFHEGMSIIERDRAAAWFAEEDTGAQVLLCSEIGSEGRNFQFASNLVMFDLPFNPDLLEQRIGRLDRIGQAHDIQIHVPYLEKTAQSVLVRWYHEGLDAFEHTCPTGRTVYDSVHDELINYLAAPESTDGFDDLIKSCRQQHDALKAQLEQGRDRLLEIHSNGGEKAQALAESIEEQDDDTSLIAFSMNLFDIVGINQDDRGENLIVLTPSDHMLVPDFPGLPEDGCTITFERDVALSREDAQFITWEHPLIRNGLDLILSGDTGSSTISLLKNKALPVGTLLLELIYVVEAQAPKQLQLNRFLPATPVRMLLDKNGNNLAAQVEFESFNRQLSAVNRHTGSKLVNAVQQDVHAILQQGEAQIAKAAQGLIDAARNEADEKLTAELSRLEALKAVNPNIRDDELAAIESNRQQVMDALAQAGWRLDALRLIVVTHQ

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 GO

Subcellular localization

Localization
Cytoplasmic

Gene Ontology (GO)

4
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0140658 An activity, driven by ATP hydrolysis, that modulates the contacts between histones and DNA, resulting in a change in chromosome architecture within the nucleosomal array, leading to chromatin remodeling.
  • GO:0016817 Catalysis of the hydrolysis of any acid anhydride.
  • GO:0006355 Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

41 records
Show feature table
Start End DB Term Name
490 644 ProSiteProfiles PS51194 Superfamilies 1 and 2 helicase C-terminal domain profile.
490 644 InterPro IPR001650 Helicase, C-terminal
150 436 FunFam G3DSA:3.40.50.10810:FF:000012 RNA polymerase-associated protein RapA
874 953 Gene3D G3DSA:6.10.140.1500 -
124 360 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
124 360 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
3 53 Pfam PF18339 RapA N-terminal Tudor like domain 1
3 53 InterPro IPR040765 RapA, N-terminal Tudor like domain 1
634 685 Gene3D G3DSA:6.10.140.2230 -
1 53 Gene3D G3DSA:2.30.30.140 -
483 633 Gene3D G3DSA:3.40.50.300 -
483 633 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
150 342 SMART SM00487 ultradead3
150 342 InterPro IPR014001 Helicase superfamily 1/2, ATP-binding domain
605 965 Pfam PF12137 RNA polymerase recycling family C-terminal
605 965 InterPro IPR022737 RNA polymerase recycling, bacterial, C-terminal
495 601 Pfam PF00271 Helicase conserved C-terminal domain
495 601 InterPro IPR001650 Helicase, C-terminal
1 966 Hamap MF_01821 RNA polymerase-associated protein RapA [rapA].
1 966 InterPro IPR023949 RNA polymerase-associated protein RapA
154 345 CDD cd18011 DEXDc_RapA
55 118 Pfam PF18337 RapA N-terminal Tudor like domain
55 118 InterPro IPR040766 RapA, N-terminal Tudor-like domain 2
150 435 Gene3D G3DSA:3.40.50.10810 -
150 435 InterPro IPR038718 SNF2-like, N-terminal domain superfamily
481 633 FunFam G3DSA:3.40.50.300:FF:000350 RNA polymerase-associated protein RapA
172 442 Pfam PF00176 SNF2-related domain
172 442 InterPro IPR000330 SNF2, N-terminal
713 790 Gene3D G3DSA:3.30.360.80 -
713 790 FunFam G3DSA:3.30.360.80:FF:000001 RNA polymerase-associated protein RapA
164 334 ProSiteProfiles PS51192 Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile.
164 334 InterPro IPR014001 Helicase superfamily 1/2, ATP-binding domain
667 687 Coils Coil Coil
488 609 CDD cd18793 SF2_C_SNF
55 114 Gene3D G3DSA:2.30.30.930 -
273 647 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
273 647 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
386 406 Coils Coil Coil
151 888 PANTHER PTHR45766 DNA ANNEALING HELICASE AND ENDONUCLEASE ZRANB3 FAMILY MEMBER
517 601 SMART SM00490 helicmild6
517 601 InterPro IPR001650 Helicase, C-terminal

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
0.937
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Surrounding area
Pocket 2 P2Rank #2
0.295
Show in viewer
Surrounding area
Pocket 3 P2Rank #3
0.2
Show in viewer
Surrounding area
Pocket 4 P2Rank #4
0.171
Show in viewer
Surrounding area
Pocket 5 P2Rank #5
0.165
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #1
0.891 Unusual size
Show in viewer
Surrounding area
Pocket 2 FPocket #29
0.539
Show in viewer
Surrounding area
Residue sets
UniProt: Binding site:156-163
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_A0A0H3GRL2
AlphaFold DB full sequence Viewing
ColabFold VK055_2516
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
AGS PDB via homolog 523.2 Da · LogP -1.51 · TPSA 262.1 Open detail RCSB PDB
BEF PDB via homolog Detail RCSB PDB
DC PDB via homolog Detail RCSB PDB
DG PDB via homolog Detail RCSB PDB
DT 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
AGS RCSB PDB P32657 523.2 Da LogP -1.51 TPSA 262.1 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
BEF RCSB PDB P32657 66.0 Da LogP 0.88 TPSA 0.0 ✓ Ro5 ✓ Clean [Be-](F)(F)F
DC RCSB PDB P32657 307.2 Da LogP -1.42 TPSA 157.1 ✓ Ro5 ✓ Clean C1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)COP(=O)(O…
DG RCSB PDB P32657 347.2 Da LogP -1.54 TPSA 185.8 ✓ Ro5 ✓ Clean c1nc2c(n1[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O)N…
DT RCSB PDB P32657 322.2 Da LogP -1.40 TPSA 151.1 ✓ Ro5 ✓ Clean CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=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.