Protein target profile

KP13_04212

Replication-associated recombination protein A

Genome: KpKP13 Gene: AHE45443.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GQY4
Length 447
Pocket druggability 0.862
Direct ligand evidence 0 53 total records
Functional annotation 0 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 (%)
41.136 Lower values reduce human off-target concern.
Human E-value
1.71e-97
Gut microbiome similarity
6.7% 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.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
89.61 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 0.862
Structure A0A0H3GQY4
Pocket Pocket 2
P2Rank 0.783
Structure A0A0H3GQY4
Pocket Pocket 1
ColabFold model
FPocket 0.767 · Pocket 1
P2Rank 0.728 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 320 / 4744 genomes with a hit
Prevalence 6.7%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MSNLSLDFSDNAFQPLAARMRPENLAQYIGQQHLLAPGKPLPRAIEAGHLHSMILWGPPGTGKTTLAEVIARYASADVERISAVTSGVKEIREAIERARQNRNAGRRTILFVDEVHRFNKSQQDAFLPHIEDGTITFIGATTENPSFELNSALLSRARVYLLKSLTTDDIERVLDQAMNDKTRGYGGQDIILPDETRRAIAELVNGDARRALNTLEMMADMAESDDSGKRVLKAELLTEIAGERSARFDNKGDRFYDLISALHKSVRGSAPDAALYWYARIITAGGDPLYVARRCLAIASEDVGNADPRAMQVAISAWDCFTRVGPAEGERAIAQAIVYLACAPKSNAVYTAFKAALADARDRPDYDVPVHLRNAPTKLMKEMGYGQEYRYAHDEPNAYAAGEQYFPQEMAQTRYYHPTNRGLEGKIGEKLAWLAEQDQNSPIKRYR

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

8 GO

Gene Ontology (GO)

8
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • 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:0006260 The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by the origin recognition complex, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
  • GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
  • GO:0008047 A molecular function regulator that increases a catalytic activity.
  • GO:0017116 Catalysis of the reaction: ATP + H2O = ADP + phosphate, in the presence of single-stranded DNA; drives the unwinding of a DNA helix.
  • GO:0000731 Synthesis of DNA that proceeds from the broken 3' single-strand DNA end and uses the homologous intact duplex as the template.
  • GO:0006261 A DNA replication process that uses parental DNA as a template for the DNA-dependent DNA polymerases that synthesize the new strands.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

25 records
Show feature table
Start End DB Term Name
165 240 Gene3D G3DSA:1.10.8.60 -
53 159 Pfam PF00004 ATPase family associated with various cellular activities (AAA)
53 159 InterPro IPR003959 ATPase, AAA-type, core
252 434 SUPERFAMILY SSF48019 post-AAA+ oligomerization domain-like
252 434 InterPro IPR008921 DNA polymerase III, clamp loader complex, gamma/delta/delta subunit, C-terminal
9 427 PANTHER PTHR13779 WERNER HELICASE-INTERACTING PROTEIN 1 FAMILY MEMBER
165 240 FunFam G3DSA:1.10.8.60:FF:000029 Replication-associated recombination protein A
188 267 Pfam PF16193 AAA C-terminal domain
188 267 InterPro IPR032423 AAA C-terminal domain
49 165 SMART SM00382 AAA_5
49 165 InterPro IPR003593 AAA+ ATPase domain
7 234 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
7 234 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
88 108 Coils Coil Coil
268 434 Pfam PF12002 MgsA AAA+ ATPase C terminal
268 434 InterPro IPR021886 MgsA AAA+ ATPase C-terminal
346 447 FunFam G3DSA:1.10.3710.10:FF:000001 Replication-associated recombination protein A
8 164 FunFam G3DSA:3.40.50.300:FF:000137 Replication-associated recombination protein A
242 345 FunFam G3DSA:1.20.272.10:FF:000001 Putative AAA family ATPase
1 164 Gene3D G3DSA:3.40.50.300 -
1 164 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
241 345 Gene3D G3DSA:1.20.272.10 -
346 447 Gene3D G3DSA:1.10.3710.10 -
165 242 CDD cd18139 HLD_clamp_RarA
29 156 CDD cd00009 AAA

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 #2
0.862
Likely same site as P2Rank 1 1.7 Å 21 shared residues 100% of smaller site
Unusual size
Show in viewer
Surrounding area

Binding pockets · P2Rank

Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Site 1 P2Rank #1
0.783
Likely same site as FPocket 2 1.7 Å 21 shared residues 100% of smaller site
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.01
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.006
Show in viewer
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_A0A0H3GQY4
AlphaFold DB full sequence Viewing
ColabFold KP13_04212
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.

53 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 3 records from similar proteins
Structural ligands 3 0 loaded crystals
Measured bioactivity 0 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
AGS PDB via homolog Detail RCSB PDB
ANP PDB via homolog Detail RCSB PDB
ZINC4806433 ZINC proposed compound · Tanimoto 0.855 Detail ZINC
ZINC12360002 ZINC proposed compound · Tanimoto 0.810 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
ADE RCSB PDB Q5SL87 135.1 Da LogP -0.06 TPSA 80.5 ✓ Ro5 ✓ Clean c1[nH]c2c(n1)c(ncn2)N
AGS RCSB PDB P35249 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 Q5SL87 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.