KpKP13 Protein target profile

Chromosomal replication initiator protein dnaA

Accession: KP13_07341

Gene: ANJ86556.1 dnaA 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3H0G8
Length 467
Pocket druggability (P2Rank · AlphaFold DB model) 0.868
Direct ligand evidence 0 51 total records
Functional annotation 0 EC 10 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
No hit
Gut microbiome similarity
4.8% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Structure confidence

ColabFold pLDDT
85.8 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) 0.868
Structure A0A0H3H0G8
Pocket Pocket 1
Druggability (FPocket) 0.094
Structure A0A0H3H0G8
Pocket Pocket 11
ColabFold model
P2Rank 0.84 · Pocket 1
FPocket 0.147 · Pocket 35
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 226 / 4744 genomes with a hit
Prevalence 4.8%

Sequence

Primary amino-acid sequence viewer.

MSLSLWQQCLARLQDELPATEFSMWIRPLQAELSDNTLALYAPNRFVLDWVRDKYLNNINGLLNDFCGADAPQLRFEVGAKPASSLQKGAVSPAAAAIPAAQVQTARAAPTIVRPGWDNVPAPAEPTYRSNVNVKHTFDNFVEGKSNQLARAAARQVADNPGGAYNPLFLYGGTGLGKTHLLHAVGNGIVARKPNAKVVYMHSERFVQDMVKALQNNAIEEFKRYYRSVDALLIDDIQFFANKERSQEEFFHTFNALLEGNQQIILTSDRYPKEINGVEDRLKSRFGWGLTVAIEPPELETRVAILMKKADENDIRLPGEVAFFIAKRLRSNVRELEGALNRVIANANFTGRAITIDFVREALRDLLALQEKLVTIDNIQKTVAEYYKIKVADLLSKRRSRSVARPRQMAMALAKELTNHSLPEIGDAFGGRDHTTVLHACRKIEQLREESHDIKEDFSNLIRTLSS

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

10 GO

Subcellular localization

Localization
Cytoplasmic

Gene Ontology (GO)

10
  • 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:0006275 Any process that modulates the frequency, rate or extent of DNA replication.
  • GO:0006270 The process in which DNA-dependent DNA replication is started; it begins when specific sequences, known as origins of replication, are recognized and bound by the origin recognition complex, followed by DNA unwinding.
  • GO:0043565 Binding to DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0003688 Binding to a DNA replication origin, a unique DNA sequence of a replicon at which DNA replication is initiated and proceeds bidirectionally or unidirectionally.
  • GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
  • GO:0008289 Binding to a lipid.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

47 records
Show feature table
Start End DB Term Name
376 465 CDD cd06571 Bac_DnaA_C
376 465 InterPro IPR013159 Chromosomal replication initiator, DnaA C-terminal
133 349 Pfam PF00308 Bacterial dnaA protein
133 349 InterPro IPR013317 Chromosomal replication initiator protein DnaA
4 64 Pfam PF11638 DnaA N-terminal domain
4 64 InterPro IPR024633 DnaA N-terminal domain
164 366 SMART SM00382 AAA_5
164 366 InterPro IPR003593 AAA+ ATPase domain
133 343 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
133 343 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
298 368 FunFam G3DSA:1.10.8.60:FF:000003 Chromosomal replication initiator protein DnaA
374 467 FunFam G3DSA:1.10.1750.10:FF:000001 Chromosomal replication initiator protein DnaA
326 346 Coils Coil Coil
1 456 PANTHER PTHR30050 CHROMOSOMAL REPLICATION INITIATOR PROTEIN DNAA
363 466 SUPERFAMILY SSF48295 TrpR-like
363 466 InterPro IPR010921 Trp repressor/replication initiator
425 444 PRINTS PR00051 Bacterial chromosomal replication initiator (DNAA) signature
425 444 InterPro IPR020591 Chromosomal replication control, initiator DnaA-like
197 211 PRINTS PR00051 Bacterial chromosomal replication initiator (DNAA) signature
197 211 InterPro IPR020591 Chromosomal replication control, initiator DnaA-like
263 290 PRINTS PR00051 Bacterial chromosomal replication initiator (DNAA) signature
263 290 InterPro IPR020591 Chromosomal replication control, initiator DnaA-like
229 243 PRINTS PR00051 Bacterial chromosomal replication initiator (DNAA) signature
229 243 InterPro IPR020591 Chromosomal replication control, initiator DnaA-like
165 185 PRINTS PR00051 Bacterial chromosomal replication initiator (DNAA) signature
165 185 InterPro IPR020591 Chromosomal replication control, initiator DnaA-like
376 444 Pfam PF08299 Bacterial dnaA protein helix-turn-helix
376 444 InterPro IPR013159 Chromosomal replication initiator, DnaA C-terminal
130 297 Gene3D G3DSA:3.40.50.300 -
130 297 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
444 464 Coils Coil Coil
298 368 Gene3D G3DSA:1.10.8.60 -
3 466 Hamap MF_00377 Chromosomal replication initiator protein DnaA [dnaA].
3 466 InterPro IPR001957 Chromosomal replication control, initiator DnaA
147 290 CDD cd00009 AAA
425 444 ProSitePatterns PS01008 DnaA protein signature.
425 444 InterPro IPR018312 Chromosomal replication control, initiator DnaA, conserved site
374 467 Gene3D G3DSA:1.10.1750.10 -
374 467 InterPro IPR010921 Trp repressor/replication initiator
2 109 FunFam G3DSA:3.30.300.180:FF:000001 Chromosomal replication initiator protein DnaA
130 297 FunFam G3DSA:3.40.50.300:FF:000103 Chromosomal replication initiator protein DnaA
375 444 SMART SM00760 bac_dnaa_c7seqb
375 444 InterPro IPR013159 Chromosomal replication initiator, DnaA C-terminal
2 109 Gene3D G3DSA:3.30.300.180 -
2 109 InterPro IPR038454 DnaA, N-terminal domain superfamily
6 465 NCBIfam TIGR00362 chromosomal replication initiator protein DnaA
6 465 InterPro IPR001957 Chromosomal replication control, initiator DnaA

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.

Download VMD script Full viewer

Loading 3D structure...

Drag to rotate — click the view, then scroll to zoom.

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
0.868
Show in viewer
Surrounding area
Pocket 2 P2Rank #2
0.088
Show in viewer
Surrounding area
Pocket 3 P2Rank #3
0.06
Show in viewer
Surrounding area
Pocket 4 P2Rank #4
0.057
Show in viewer
Surrounding area
Pocket 5 P2Rank #5
0.039
Show in viewer
Surrounding area
Residue sets
UniProt: Binding site:175-175
UniProt: Binding site:177-177
UniProt: Binding site:178-178
UniProt: Binding site:179-179
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_A0A0H3H0G8
AlphaFold DB full sequence Viewing
ColabFold KP13_07341
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.

51 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 1 records from similar proteins
Structural ligands 1 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
ACP PDB via homolog 505.2 Da · LogP -1.52 · TPSA 269.9 Open detail RCSB PDB
ZINC105469665 ZINC proposed compound · Tanimoto 0.873 Detail ZINC
ZINC13527614 ZINC proposed compound · Tanimoto 0.873 Detail ZINC
ZINC219330894 ZINC proposed compound · Tanimoto 0.873 Detail ZINC
ZINC3873852 ZINC proposed compound · Tanimoto 0.873 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
ACP RCSB PDB O66659 505.2 Da LogP -1.52 TPSA 269.9 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.