Protein target profile

VK055_0072

holliday junction DNA helicase RuvB

Genome: KpATCC43816 Gene: ruvB AIK78700.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3H053
Length 336
Pocket druggability 0.932
Direct ligand evidence 0 159 total records
Functional annotation 1 EC 9 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 (%)
29.752 Lower values reduce human off-target concern.
Human E-value
2.7e-07
Gut microbiome similarity
89.9% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
95.238 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
92.63 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 0.932
Structure A0A0H3H053
Pocket Pocket 1
P2Rank 0.819
Structure A0A0H3H053
Pocket Pocket 1
ColabFold model
FPocket 0.54 · Pocket 2
P2Rank 0.879 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 4266 / 4744 genomes with a hit
Prevalence 89.9%

Cross-references

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

Chemistry

ChEMBL CHEMBL3747448 ChEMBL JDP ChEMBL CHEMBL3746179 ChEMBL CHEMBL4280801 ChEMBL CHEMBL6064283 ChEMBL CHEMBL4555451 ChEMBL OJA ChEMBL CHEMBL4553677 ChEMBL CHEMBL3747049 ChEMBL CHEMBL4535337 ChEMBL CHEMBL4441270 ChEMBL CHEMBL5937029 ChEMBL CHEMBL4445673 ChEMBL CHEMBL4453010 ChEMBL CHEMBL5189708 ChEMBL CHEMBL5966795 ChEMBL CHEMBL4551165 ChEMBL CHEMBL4543206 ChEMBL CHEMBL4463657 ChEMBL CHEMBL5192118 ChEMBL CHEMBL4580172 ChEMBL CHEMBL4846448 ChEMBL CHEMBL4460205 ChEMBL CHEMBL4438398 ChEMBL CHEMBL4459139 ChEMBL CHEMBL4451017 ChEMBL CHEMBL5175854 ChEMBL CHEMBL3787674 ChEMBL CHEMBL4461505 ChEMBL CHEMBL4463689 ChEMBL CHEMBL4558932 ChEMBL CHEMBL3747647 ChEMBL CHEMBL4277404 ChEMBL CHEMBL4446356 ChEMBL CHEMBL3696924 ChEMBL CHEMBL4456523 ChEMBL CHEMBL4535642 ChEMBL CHEMBL5184848 ChEMBL CHEMBL4862740 ChEMBL CHEMBL3696915 ChEMBL CHEMBL6010286 ChEMBL CHEMBL5199985 ChEMBL CHEMBL4288865 ChEMBL CHEMBL5184774 ChEMBL CHEMBL5180155 ChEMBL CHEMBL5205850 ChEMBL CHEMBL4871978 ChEMBL CHEMBL4858461 ChEMBL CHEMBL4854511 ChEMBL CHEMBL3696925 ChEMBL CHEMBL3745888 ChEMBL CHEMBL5198263 ChEMBL CHEMBL3746353 ChEMBL CHEMBL5903736 ChEMBL CHEMBL4455739 ChEMBL CHEMBL5893353 ChEMBL CHEMBL6010728 ChEMBL CHEMBL4872975 ChEMBL CHEMBL4876550 ChEMBL CHEMBL4848009 ChEMBL CHEMBL4871208 ChEMBL CHEMBL6015615 ChEMBL CHEMBL4859176 ChEMBL CHEMBL3746650 ChEMBL CHEMBL5176940 ChEMBL CHEMBL3747498 ChEMBL CHEMBL4847081 ChEMBL CHEMBL5175776 ChEMBL CHEMBL4280546 ChEMBL CHEMBL4291440 ChEMBL CHEMBL4573319 ChEMBL CHEMBL5780988 ChEMBL CHEMBL5845840 ChEMBL CHEMBL3746912 ChEMBL CHEMBL5798108 ChEMBL CHEMBL5862582 ChEMBL CHEMBL5913286 ChEMBL CHEMBL6049771 ChEMBL CHEMBL4864700 ChEMBL CHEMBL4858094 ChEMBL CHEMBL4877447 ChEMBL CHEMBL4276697 ChEMBL CHEMBL4439188 ChEMBL CHEMBL5931306 ChEMBL CHEMBL4288427 ChEMBL CHEMBL4530376 ChEMBL CHEMBL5810576 ChEMBL CHEMBL5870048 ChEMBL CHEMBL4461462 ChEMBL CHEMBL5819590 ChEMBL CHEMBL5861026 ChEMBL CHEMBL5946783 ChEMBL CHEMBL5963984 ChEMBL CHEMBL3746000 ChEMBL CHEMBL3696861 ChEMBL CHEMBL3696917 ChEMBL CHEMBL5751058 ChEMBL CHEMBL5783148 ChEMBL CHEMBL5889892 ChEMBL CHEMBL6032099

Sequence

Primary amino-acid sequence viewer.

MIEADRLVSADSSGFEEAADRAIRPKLLAEYVGQPQVRSQMEIFIQAAKLRGDALDHLLIFGPPGLGKTTLANIVANEMGVNLRTTSGPVLEKAGDLAAMLTNLEPHDVLFIDEIHRLSPVVEEVLYPAMEDYQLDIMIGEGPAARSIKIDLPPFTLIGATTRAGSLTSPLRDRFGIVQRLEFYQIPDLQHIVSRSARHMGLEMSDEGALEVARRSRGTPRIANRLLRRVRDFAEVRHDGTISADIAAQALDMLNVDAEGFDYMDRKLLLAVIDKFFGGPVGLDNLAAAIGEERETIEDVLEPYLIQQGFLQRTPRGRMATVRAWNHFGITPPEMP

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 9 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

9
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0006310 Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Interchromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.
  • GO:0006281 The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
  • GO:0016887 Catalysis of the reaction: ATP + H2O = ADP + H+ phosphate. ATP hydrolysis is used in some reactions as an energy source, for example to catalyze a reaction or drive transport against a concentration gradient.
  • GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
  • GO:0009378 Unwinding a DNA helix of DNA containing four-way junctions, including Holliday junctions, driven by ATP hydrolysis.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0048476 An endodeoxyribonuclease complex that resolves the 4-way DNA intermediates of a Holliday junction into two separate duplex DNA molecules. Can be branch-migration associated.
  • GO:0000400 Binding to a DNA segment containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

27 records
Show feature table
Start End DB Term Name
186 258 Gene3D G3DSA:1.10.8.60 -
2 334 PANTHER PTHR42848 -
2 334 InterPro IPR004605 Holliday junction branch migration complex subunit RuvB
260 333 SUPERFAMILY SSF46785 Winged helix DNA-binding domain
260 333 InterPro IPR036390 Winged helix DNA-binding domain superfamily
54 181 SMART SM00382 AAA_5
54 181 InterPro IPR003593 AAA+ ATPase domain
27 329 NCBIfam TIGR00635 Holliday junction DNA helicase RuvB
27 329 InterPro IPR004605 Holliday junction branch migration complex subunit RuvB
42 178 CDD cd00009 AAA
260 336 Gene3D G3DSA:1.10.10.10 -
260 336 InterPro IPR036388 Winged helix-like DNA-binding domain superfamily
184 257 Pfam PF17864 RuvB AAA lid domain
184 257 InterPro IPR041445 RuvB, AAA lid domain
186 258 FunFam G3DSA:1.10.8.60:FF:000023 Holliday junction ATP-dependent DNA helicase RuvB
1 336 Hamap MF_00016 Holliday junction branch migration complex subunit RuvB [ruvB].
1 336 InterPro IPR004605 Holliday junction branch migration complex subunit RuvB
260 336 FunFam G3DSA:1.10.10.10:FF:000086 Holliday junction ATP-dependent DNA helicase RuvB
22 183 FunFam G3DSA:3.40.50.300:FF:000073 Holliday junction ATP-dependent DNA helicase RuvB
259 328 Pfam PF05491 RuvB C-terminal winged helix domain
259 328 InterPro IPR008823 RuvB C-terminal winged helix domain
22 183 Gene3D G3DSA:3.40.50.300 -
22 183 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
23 181 Pfam PF05496 Holliday junction DNA helicase RuvB P-loop domain
23 181 InterPro IPR008824 RuvB-like P-loop domain
23 255 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
23 255 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase

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
0.932
Likely same site as P2Rank 1 4.0 Å 18 shared residues 95% 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
0.819
Likely same site as FPocket 1 4.0 Å 18 shared residues 95% of smaller site
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.021
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.015
Show in viewer
Surrounding area
Site 4 P2Rank #4
0.004
Show in viewer
Surrounding area
Residue sets
UniProt: Binding site:131-133
UniProt: Binding site:174-174
UniProt: Binding site:184-184
UniProt: Binding site:221-221
UniProt: Binding site:23-23
UniProt: Binding site:24-24
UniProt: Binding site:294-294
UniProt: Binding site:313-313
UniProt: Binding site:318-318
UniProt: Binding site:65-65
UniProt: Binding site:68-68
UniProt: Binding site:69-69
UniProt: Binding site:70-70
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_A0A0H3H053
AlphaFold DB full sequence Viewing
ColabFold VK055_0072
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.

159 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 109 records from similar proteins
Structural ligands 9 0 loaded crystals
Measured bioactivity 100 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
ADE PDB via homolog 135.1 Da · LogP -0.06 · TPSA 80.5 Open detail RCSB PDB
AF3 PDB via homolog Detail RCSB PDB
AGS PDB via homolog Detail RCSB PDB
ANP PDB via homolog Detail RCSB PDB
AWD 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
ADE RCSB PDB Q5SL87 135.1 Da LogP -0.06 TPSA 80.5 ✓ Ro5 ✓ Clean c1[nH]c2c(n1)c(ncn2)N
AF3 RCSB PDB Q01853 84.0 Da LogP 0.88 TPSA 0.0 ✓ Ro5 ✓ Clean F[Al](F)F
AGS RCSB PDB G0S6Y2 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)…
ANP RCSB PDB P55072 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)…
AWD RCSB PDB P55072 237.3 Da LogP 1.60 TPSA 35.6 ✓ Ro5 ✓ Clean CN1CCN(CC1)C(=O)Nc2ccc(cc2)F
EJQ RCSB PDB P55072 222.3 Da LogP 1.86 TPSA 32.3 ✓ Ro5 ✓ Clean c1cc(ccc1NC(=O)CN2CCCC2)F
EJW RCSB PDB P55072 175.2 Da LogP 1.08 TPSA 53.7 ✓ Ro5 ✓ Clean c1ccc(cc1)c2cc(on2)C[NH3+]
ELN RCSB PDB P55072 194.6 Da LogP 2.19 TPSA 52.9 ✓ Ro5 ✓ Clean c1cc(ccc1NC(=O)CC#N)Cl
ELQ RCSB PDB P55072 240.3 Da LogP 1.35 TPSA 23.6 ✓ Ro5 ✓ Clean CN1CCN(CC1)C(=O)c2ccc(c(c2)F)F

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.