KpKP13 Protein target profile

ATP-dependent DNA helicase recG

Accession: KP13_00162

Gene: recG AHE42082.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3H4K6
Length 693
Pocket druggability (P2Rank · AlphaFold DB model) 0.893
Direct ligand evidence 0 57 total records
Functional annotation 1 EC 8 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 (%)
37.975 Lower values reduce human off-target concern.
Human E-value
4.92e-06
Gut microbiome similarity
3.9% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Structure confidence

ColabFold pLDDT
85.59 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) 0.893
Structure A0A0H3H4K6
Pocket Pocket 1
Druggability (FPocket) 0.673
Structure A0A0H3H4K6
Pocket Pocket 25
ColabFold model
P2Rank 0.874 · Pocket 1
FPocket 0.881 · Pocket 4
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 185 / 4744 genomes with a hit
Prevalence 3.9%

Sequence

Primary amino-acid sequence viewer.

MSGRLLDAVPLSSLTGVGAAQSSKLAKIGLHTVQDLLLHLPLRYEDRTHLYPIAELLPGVYATVEGEVLNSNITFGGRRMMTCQISDGTGILTMRFFNFNAAMKNSLATGRRVLAYGEAKRGKYGAEMIHPEYRVQGDMSTPELQETLTPVYPTTEGIKQATLRKLTDQALELLETCAISELLPPELAQGMMSLPEALRTLHRPPPSLQLSELESGKHPAQQRLILEELLAHNLSMLALRAGAQRYHALPLGANDTLKNQLLASLPFKPTGAQARVTAEIEHDMALDVPMMRLVQGDVGSGKTLVAALAALRAIVHGKQVALMAPTELLAEQHANNFRSWFEPLGIEVGWLAGKQKGKARQAQQEAIASGEVQMIVGTHAIFQEQVQFNGLALVIIDEQHRFGVHQRLALWEKGQQQGFHPHQLIMTATPIPRTLAMTAYADLDTSIIDELPPGRTPVTTVAIPDTRRSDIIDRVRNACTHEGRQAYWVCTLIEESDLLEAQAAEATWEELKLALPELNIGLVHGRMKPAEKQAVMQAFKQGEMHLLVATTVIEVGVDVPNSSLMIIENPERLGLAQLHQLRGRVGRGAVASHCVLLYKSPLSKTAQKRLQVLRDSNDGFVIAQKDLEIRGPGELLGTRQTGNAEFKVADLLRDQAMIPDVQRIARHIHERYPLQAQALIERWMPETERYSNA

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 8 GO

Subcellular localization

Localization
Cytoplasmic

Enzyme Commission (EC)

1

Gene Ontology (GO)

8
  • GO:0003676 Binding to a nucleic acid.
  • GO:0003678 Unwinding of a DNA helix, driven by ATP hydrolysis.
  • 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:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0043138 Unwinding a DNA helix in the direction 5' to 3', driven by ATP hydrolysis.
  • 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).

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

38 records
Show feature table
Start End DB Term Name
457 615 CDD cd18811 SF2_C_RecG
208 450 FunFam G3DSA:3.40.50.300:FF:000715 ATP-dependent DNA helicase RecG
617 672 Pfam PF19833 ATP-dependent DNA helicase RecG, domain 3, C-terminal
617 672 InterPro IPR045562 ATP-dependent DNA helicase RecG, domain 3, C-terminal
265 459 SMART SM00487 ultradead3
265 459 InterPro IPR014001 Helicase superfamily 1/2, ATP-binding domain
482 628 ProSiteProfiles PS51194 Superfamilies 1 and 2 helicase C-terminal domain profile.
482 628 InterPro IPR001650 Helicase, C-terminal
480 588 Pfam PF00271 Helicase conserved C-terminal domain
480 588 InterPro IPR001650 Helicase, C-terminal
209 453 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
209 453 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
63 135 CDD cd04488 RecG_wedge_OBF
15 171 Pfam PF17191 RecG wedge domain
15 171 InterPro IPR033454 RecG, wedge domain
292 653 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
292 653 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
224 452 CDD cd17992 DEXHc_RecG
5 684 PANTHER PTHR47964 ATP-DEPENDENT DNA HELICASE HOMOLOG RECG, CHLOROPLASTIC
5 684 InterPro IPR047112 ATP-dependent DNA helicase RecG/Transcription-repair-coupling factor
505 589 SMART SM00490 helicmild6
505 589 InterPro IPR001650 Helicase, C-terminal
47 140 FunFam G3DSA:2.40.50.140:FF:000134 ATP-dependent DNA helicase RecG
9 175 SUPERFAMILY SSF50249 Nucleic acid-binding proteins
9 175 InterPro IPR012340 Nucleic acid-binding, OB-fold
28 664 NCBIfam TIGR00643 ATP-dependent DNA helicase RecG
28 664 InterPro IPR004609 ATP-dependent DNA helicase RecG
457 630 FunFam G3DSA:3.40.50.300:FF:000391 ATP-dependent DNA helicase RecG
208 450 Gene3D G3DSA:3.40.50.300 -
208 450 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
47 140 Gene3D G3DSA:2.40.50.140 -
47 140 InterPro IPR012340 Nucleic acid-binding, OB-fold
293 433 Pfam PF00270 DEAD/DEAH box helicase
293 433 InterPro IPR011545 DEAD/DEAH box helicase domain
283 448 ProSiteProfiles PS51192 Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile.
283 448 InterPro IPR014001 Helicase superfamily 1/2, ATP-binding domain
457 630 Gene3D G3DSA:3.40.50.300 -
457 630 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 · P2Rank

Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Pocket 1 P2Rank #1
0.893
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Surrounding area
Pocket 2 P2Rank #2
0.838
Likely same site as FPocket 49 5.7 Å 15 shared residues 62% of smaller site
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Surrounding area
Pocket 3 P2Rank #3
0.377
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Surrounding area
Pocket 4 P2Rank #4
0.089
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Surrounding area
Pocket 5 P2Rank #5
0.079
Likely same site as FPocket 6 2.2 Å 10 shared residues 83% of smaller site
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Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #25
0.673 Unusual size
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Surrounding area
Pocket 2 FPocket #6
0.455
Likely same site as P2Rank 5 2.2 Å 10 shared residues 83% of smaller site
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Surrounding area
Pocket 3 FPocket #49
0.391 Unusual size
Likely same site as P2Rank 2 5.7 Å 15 shared residues 62% of smaller site
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Surrounding area
Pocket 4 FPocket #37
0.375
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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_A0A0H3H4K6
AlphaFold DB full sequence Viewing
ColabFold KP13_00162
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.

57 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 7 records from similar proteins
Structural ligands 2 0 loaded crystals
Measured bioactivity 5 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
ANP PDB via homolog Detail RCSB PDB
CHEMBL1471192 ChEMBL via homolog · pchembl 7.25 (~56.2 nM) Detail ChEMBL
CHEMBL1560762 ChEMBL via homolog · pchembl 6.85 (~141.3 nM) Detail ChEMBL
CHEMBL1446521 ChEMBL via homolog · pchembl 6.50 (~316.2 nM) Detail ChEMBL

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 G0S0B9 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 Q9NR30 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)…

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.