Protein target profile

KP13_03293

Deoxyribodipyrimidine photo-lyase

Genome: KpKP13 Gene: phrB AHE45672.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GK13
Length 480
Pocket druggability 0.867
Direct ligand evidence 0 53 total records
Functional annotation 1 EC 5 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 (%)
27.959 Lower values reduce human off-target concern.
Human E-value
7.569999999999999e-42
Gut microbiome similarity
2.4% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Localization

Localization
Unknown

Structure confidence

ColabFold pLDDT
96.03 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 0.867
Structure A0A0H3GK13
Pocket Pocket 1
P2Rank 0.956
Structure A0A0H3GK13
Pocket Pocket 1
ColabFold model
FPocket 0.857 · Pocket 1
P2Rank 0.959 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 116 / 4744 genomes with a hit
Prevalence 2.4%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MATHLVWLRTDLRIHDNLALAAACRDPQAQVLALYIATPGQWREHHLAPRQAAFIASHLQSLHAALAERGIPLWVEEADDFTASVERLADFCQQHQVSHLFYNYQYEFNERQRDAAVENTLRDVICQGFDDSVLLPPGSVLTGGGEMYKVFTPFKNAFIRRLRDGLPACVAAPKPRQAPARQAPPLPELNYPQTPFDGLLFAADEKTALARLRAFCQQAAADYEGQRDFPAVEGTSRLSPCLAIGVLSPRQCLHRLLTEHPAALDGGAGATWLNELIWREFYRHLMVYYPKLCKGRPFTAWTDKVAWRAEEASLQAWQRGETGFPIVDAAMRQLNATGWMHNRLRMIVASFLTKDLRLDWRAGERYFMSQLIDGDLAANNGGWQWAASTGTDAAPYFRIFNPTTQGEKFDKQGVFIRRWLPELAKVPEKALHQPWAWADKQGITLDYSRPIVDHKQARQETLAAWEAARKGITPPPDGGS

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

5
  • GO:0003904 Catalysis of the reaction: cyclobutadipyrimidine (in DNA) = 2 pyrimidine residues (in DNA). This reaction represents the reactivation of irradiated DNA by light.
  • GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
  • GO:0071949 Binding to the oxidized form, FAD, of flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
  • GO:0000719 The repair of UV-induced T-T, C-T and C-C dimers by directly reversing the damage to restore the original pyrimidines.
  • GO:0009416 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a light stimulus, electromagnetic radiation of wavelengths classified as infrared, visible or ultraviolet light.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

29 records
Show feature table
Start End DB Term Name
2 134 ProSiteProfiles PS51645 Photolyase/cryptochrome alpha/beta domain profile.
2 134 InterPro IPR006050 DNA photolyase, N-terminal
5 168 Pfam PF00875 DNA photolyase
5 168 InterPro IPR006050 DNA photolyase, N-terminal
322 334 ProSitePatterns PS00394 DNA photolyases class 1 signature 1.
322 334 InterPro IPR018394 Cryptochrome/DNA photolyase class 1, conserved site, C-terminal
290 472 FunFam G3DSA:1.10.579.10:FF:000003 Deoxyribodipyrimidine photo-lyase
5 203 Gene3D G3DSA:3.40.50.620 HUPs
5 203 InterPro IPR014729 Rossmann-like alpha/beta/alpha sandwich fold
132 286 Gene3D G3DSA:1.25.40.80 -
272 466 Pfam PF03441 FAD binding domain of DNA photolyase
272 466 InterPro IPR005101 Cryptochrome/DNA photolyase, FAD-binding domain
197 470 SUPERFAMILY SSF48173 Cryptochrome/photolyase FAD-binding domain
197 470 InterPro IPR036134 Cryptochrome/DNA photolyase, FAD-binding domain-like superfamily
342 361 ProSitePatterns PS00691 DNA photolyases class 1 signature 2.
342 361 InterPro IPR018394 Cryptochrome/DNA photolyase class 1, conserved site, C-terminal
5 468 PANTHER PTHR11455 CRYPTOCHROME
5 468 InterPro IPR002081 Cryptochrome/DNA photolyase class 1
381 395 PRINTS PR00147 DNA photolyase signature
381 395 InterPro IPR002081 Cryptochrome/DNA photolyase class 1
322 338 PRINTS PR00147 DNA photolyase signature
322 338 InterPro IPR002081 Cryptochrome/DNA photolyase class 1
342 360 PRINTS PR00147 DNA photolyase signature
342 360 InterPro IPR002081 Cryptochrome/DNA photolyase class 1
143 159 PRINTS PR00147 DNA photolyase signature
143 159 InterPro IPR002081 Cryptochrome/DNA photolyase class 1
3 197 SUPERFAMILY SSF52425 Cryptochrome/photolyase, N-terminal domain
3 197 InterPro IPR036155 Cryptochrome/photolyase, N-terminal domain superfamily
290 472 Gene3D G3DSA:1.10.579.10 DNA Cyclobutane Dipyrimidine Photolyase, subunit A, domain 3

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
0.867
Likely same site as P2Rank 2 1.2 Å 33 shared residues 97% 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
0.956
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.922
Likely same site as FPocket 1 1.2 Å 33 shared residues 97% of smaller site
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.084
Show in viewer
Surrounding area
Site 4 P2Rank #4
0.001
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Surrounding area
Site 5 P2Rank #5
0.001
Show in viewer
Surrounding area
Residue sets
UniProt: Binding site:223-223
UniProt: Binding site:235-239
UniProt: Binding site:272-272
UniProt: Binding site:275-282
UniProt: Binding site:373-375
UniProt: Site:307-307 Electron transfer via tryptophanyl radical
UniProt: Site:360-360 Electron transfer via tryptophanyl radical
UniProt: Site:383-383 Electron transfer via tryptophanyl radical
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_A0A0H3GK13
AlphaFold DB full sequence Viewing
ColabFold KP13_03293
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
ANP PDB via homolog 506.2 Da · LogP -2.06 · TPSA 281.9 Open detail RCSB PDB
HDF PDB via homolog Detail RCSB PDB
TDR PDB via homolog Detail RCSB PDB
ZINC100069844 ZINC proposed compound · Tanimoto 1.000 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
ANP RCSB PDB Q43125 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)…
HDF RCSB PDB P05327 363.3 Da LogP -2.03 TPSA 168.9 1 viol. ✓ Clean c1cc2c(cc1O)N(C3=NC(=O)NC(=O)C3=C2)C[C@H]([C@@H…
TDR RCSB PDB P61497 126.1 Da LogP -0.63 TPSA 65.7 ✓ Ro5 ✓ Clean CC1=CNC(=O)NC1=O

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.