Protein target profile

HT085_RS00005

chromosomal replication initiator protein DnaA

Genome: NZ_AP023069.1 Gene: N776_09350 WHOF_00001 NGO_0001 TUM19854C_00010 dnaA WHOF_00422 E8M63_03550 ESCNG_30050 3D evidence: AlphaFold DB model UniProt Q5FAJ2 UniProt A0AA44U8W6 UniProt A0A1D3GRD6
Length 518
Direct ligand evidence 0 51 total records
Functional annotation 0 EC 9 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
No hit
Gut microbiome off-target
Hit

Essentiality

Essential (DEG)
Y

Localization

Localization
Cytoplasmic

Binding-site evidence

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 Medium
Structure
Pocket

Sequence

Primary amino-acid sequence viewer.

MTLAEFWPLCLRRLHDMLPHGQFAQWIAPLTVGEEGGVWVVYGKNQFACNMLKSQFAGKIEAVREELAAGRPAFVFKPGEGVRYEMAAVEGAVEPAEPSLHAGSEEMPVQEVLLDELPSEKPVKPAASKTAADILAERMKNLPHEPRQAAGPASRPESAAVAKARTDAQRDAEEARYEQTNLSPDYTFDTLVEGKGNRLAAAAAQAIAENPGQSYNPFFLYGSTGLGKTHLVQAVGNELLKNRPDAKVRYMHSDDYIRSFMKAVRNNTYDVFKQQYKQYDLLIIDDIQFIKGKDRTMEEFFYLYNHFHNEKKQLILTCDVLPAKIEGMDDRLKSRFSWGLTLELEPPELEMRIAILQKKAEAAGISIEDEAALFIANLIRSNVRELEGAFNRVGASSRFMNRPVIDIDLARTALQDIIAEKHKVITADIIIDAVAKYYRIKISDVLGKKRTRNIARPRQVAMSLTKELTTLSLPSIGDSFGGRDHTTVMHGIRAVAKLREEDPELAQDYEKLLILIQN

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

9 GO

Gene Ontology (GO)

9
  • 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: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: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:0006275 Any process that modulates the frequency, rate or extent of DNA replication.
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • 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.

46 records
Show feature table
Start End DB Term Name
1 508 PANTHER PTHR30050 CHROMOSOMAL REPLICATION INITIATOR PROTEIN DNAA
348 419 FunFam G3DSA:1.10.8.60:FF:000003 Chromosomal replication initiator protein DnaA
140 180 MobiDBLite mobidb-lite consensus disorder prediction
4 102 Gene3D G3DSA:3.30.300.180 -
4 102 InterPro IPR038454 DnaA, N-terminal domain superfamily
180 347 Gene3D G3DSA:3.40.50.300 -
180 347 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
214 344 SMART SM00382 AAA_5
214 344 InterPro IPR003593 AAA+ ATPase domain
414 517 SUPERFAMILY SSF48295 TrpR-like
414 517 InterPro IPR010921 Trp repressor/replication initiator
182 397 Pfam PF00308 Bacterial dnaA protein
182 397 InterPro IPR013317 Chromosomal replication initiator protein DnaA
4 517 Hamap MF_00377 Chromosomal replication initiator protein DnaA [dnaA].
4 517 InterPro IPR001957 Chromosomal replication control, initiator DnaA
180 347 FunFam G3DSA:3.40.50.300:FF:000668 Chromosomal replication initiator protein DnaA
7 513 NCBIfam TIGR00362 chromosomal replication initiator protein DnaA
7 513 InterPro IPR001957 Chromosomal replication control, initiator DnaA
419 516 Gene3D G3DSA:1.10.1750.10 -
419 516 InterPro IPR010921 Trp repressor/replication initiator
428 495 Pfam PF08299 Bacterial dnaA protein helix-turn-helix
428 495 InterPro IPR013159 Chromosomal replication initiator, DnaA C-terminal
5 62 Pfam PF11638 DnaA N-terminal domain
5 62 InterPro IPR024633 DnaA N-terminal domain
348 418 Gene3D G3DSA:1.10.8.60 -
419 516 FunFam G3DSA:1.10.1750.10:FF:000006 Chromosomal replication initiator protein DnaA
476 495 ProSitePatterns PS01008 DnaA protein signature.
476 495 InterPro IPR018312 Chromosomal replication control, initiator DnaA, conserved site
313 340 PRINTS PR00051 Bacterial chromosomal replication initiator (DNAA) signature
313 340 InterPro IPR020591 Chromosomal replication control, initiator DnaA-like
279 293 PRINTS PR00051 Bacterial chromosomal replication initiator (DNAA) signature
279 293 InterPro IPR020591 Chromosomal replication control, initiator DnaA-like
476 495 PRINTS PR00051 Bacterial chromosomal replication initiator (DNAA) signature
476 495 InterPro IPR020591 Chromosomal replication control, initiator DnaA-like
247 261 PRINTS PR00051 Bacterial chromosomal replication initiator (DNAA) signature
247 261 InterPro IPR020591 Chromosomal replication control, initiator DnaA-like
215 235 PRINTS PR00051 Bacterial chromosomal replication initiator (DNAA) signature
215 235 InterPro IPR020591 Chromosomal replication control, initiator DnaA-like
426 495 SMART SM00760 bac_dnaa_c7seqb
426 495 InterPro IPR013159 Chromosomal replication initiator, DnaA C-terminal
211 340 CDD cd00009 AAA
428 512 CDD cd06571 Bac_DnaA_C
428 512 InterPro IPR013159 Chromosomal replication initiator, DnaA C-terminal
164 178 MobiDBLite mobidb-lite consensus disorder prediction
181 393 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
181 393 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.
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
0.58
Likely same site as P2Rank 1 4.9 Å 22 shared residues 92% of smaller site
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Surrounding area
Site 2 FPocket #7
0.378
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Surrounding area
Site 3 FPocket #2
0.307
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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
0.738
Likely same site as FPocket 1 4.9 Å 22 shared residues 92% of smaller site
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Surrounding area
Site 2 P2Rank #2
0.05
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Surrounding area
Site 3 P2Rank #3
0.013
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Surrounding area
All structural evidence 0 experimental · 1 predicted

Structural evidence

0 + 1

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 HT085_RS00005
AlphaFold DB full sequence Viewing

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.