KpKP13 Protein target profile

putative metal-dependent phosphohydrolase

Accession: KP13_03062

Gene: AHE44935.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GRT1
Length 510
Pocket druggability (P2Rank · AlphaFold DB model) 0.982
Direct ligand evidence 0 74 total records
Functional annotation 0 EC 0 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
Hit
Human identity (%)
52.174 Lower values reduce human off-target concern.
Human E-value
5.35e-12
Gut microbiome similarity
0.1% 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.

Structure confidence

ColabFold pLDDT
94.99 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) 0.982
Structure A0A0H3GRT1
Pocket Pocket 1
Druggability (FPocket) 0.347
Structure A0A0H3GRT1
Pocket Pocket 9
ColabFold model
P2Rank 0.967 · Pocket 1
FPocket 0.363 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 3 / 4744 genomes with a hit
Prevalence 0.1%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MDFENELTSKILDPIHGTIRLTTLEIAFINHPLFQRLRNIKQNSFLYKVFPSAVHSRFEHSLGVLHLSSEILNNLRLNAIRYQKKYDDGHVFGHIDQIPKHNIQELRLAALMHDIGHGPVSHQFESFMPGKHEFSDVLPTAYHSIIDVLSKPEQKVEHEQLSLLFSLMIYHDLRKQGKVDDEINIENVLKIIEKRYGDQQIIEEINGKATDILPLMTSIISSCPIDADRMDYLLRDGYFSGVKCGIYDYNRLFMSIVPVEEQGKLYLAYKESGIDSIAEFIGARSSLFSQVYYHKTNRAFATMLSTLCEIMQSKDPQNVIIADVTDRIVDHSDESFIDALKEFYLSCSDDYFLNDKVGEWIDISDTEAVNKKILHDIINRHPWSKVYEAKHSVYKANIVDKENKAWKSQLTGLLTSVLQPHFKPHEFAVDIVSDCAFKDLDKTEVKLLVKDLKNRYEIKPLIECGDKLNQYQIIKYCIRVFVDRDIKERVTPEITYKINDIVVKQIALLN

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

Subcellular localization

Localization
Cytoplasmic

No GO or EC annotations are currently loaded for this protein.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

9 records
Show feature table
Start End DB Term Name
11 439 PANTHER PTHR11373 DEOXYNUCLEOSIDE TRIPHOSPHATE TRIPHOSPHOHYDROLASE
53 242 SMART SM00471 hd_13
53 242 InterPro IPR003607 HD/PDEase domain
10 483 SUPERFAMILY SSF109604 HD-domain/PDEase-like
8 381 Gene3D G3DSA:1.10.3210.10 Hypothetical protein af1432
55 253 CDD cd00077 HDc
55 253 InterPro IPR003607 HD/PDEase domain
57 235 Pfam PF01966 HD domain
57 235 InterPro IPR006674 HD domain

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
0.982
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Surrounding area
Pocket 2 P2Rank #2
0.223
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Surrounding area
Pocket 3 P2Rank #3
0.056
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Surrounding area
Pocket 4 P2Rank #4
0.045
Likely same site as FPocket 9 1.3 Å 5 shared residues 100% of smaller site
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Surrounding area
Pocket 5 P2Rank #5
0.032
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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 #9
0.347
Likely same site as P2Rank 4 1.3 Å 5 shared residues 100% of smaller site
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_A0A0H3GRT1
AlphaFold DB full sequence Viewing
ColabFold KP13_03062
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.

74 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 24 records from similar proteins
Structural ligands 23 0 loaded crystals
Measured bioactivity 1 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
0KX PDB via homolog 466.2 Da · LogP -1.61 · TPSA 253.0 Open detail RCSB PDB
1FZ PDB via homolog Detail RCSB PDB
3PO PDB via homolog Detail RCSB PDB
CZF PDB via homolog Detail RCSB PDB
DCP PDB via homolog Detail RCSB PDB

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
0KX RCSB PDB Q9Y3Z3 466.2 Da LogP -1.61 TPSA 253.0 2 viol. ✓ Clean C1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)COP(=O)(N…
1FZ RCSB PDB Q9Y3Z3 481.2 Da LogP -1.59 TPSA 246.9 1 viol. ✓ Clean CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O…
3PO RCSB PDB Q9Y3Z3 258.0 Da LogP -0.69 TPSA 170.8 ✓ Ro5 ✓ Clean OP(=O)(O)OP(=O)(O)OP(=O)(O)O
CZF RCSB PDB Q9Y3Z3 524.2 Da LogP -2.62 TPSA 293.0 3 viol. ✓ Clean c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O…
DCP RCSB PDB Q9Y3Z3 467.2 Da LogP -1.18 TPSA 250.2 2 viol. ✓ Clean C1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)CO[P@@](=…
DG3 RCSB PDB Q9Y3Z3 491.2 Da LogP -0.28 TPSA 258.6 2 viol. ✓ Clean c1nc2c(n1[C@H]3CC[C@H](O3)CO[P@@](=O)(O)O[P@](=…
DGT RCSB PDB I3LG77 507.2 Da LogP -1.31 TPSA 278.9 3 viol. ✓ Clean c1nc2c(n1[C@H]3C[C@@H]([C@H](O3)CO[P@@](=O)(O)O…
DTP RCSB PDB Q9Y3Z3 491.2 Da LogP -0.60 TPSA 258.9 2 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3C[C@@H]([C@H](O3)CO[P@]…
DUT RCSB PDB Q9Y3Z3 468.1 Da LogP -1.47 TPSA 244.1 2 viol. ✓ Clean C1[C@@H]([C@H](O[C@H]1N2C=CC(=O)NC2=O)CO[P@@](=…
DZ4 RCSB PDB Q9Y3Z3 490.2 Da LogP -1.03 TPSA 261.7 2 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3C[C@@H]([C@H](O3)CO[P@@…
F6G RCSB PDB Q9Y3Z3 470.2 Da LogP -1.90 TPSA 260.0 2 viol. ✓ Clean C1[C@@H]([C@H](O[C@H]1N2CN=C(NC2=O)N)COP(=O)(O)…
GTF RCSB PDB Q9Y3Z3 503.1 Da LogP -0.94 TPSA 250.2 3 viol. ✓ Clean C1=CN(C(=O)N=C1N)[C@H]2C([C@@H]([C@H](O2)COP(=O…
HDV RCSB PDB Q9Y3Z3 523.2 Da LogP -0.34 TPSA 258.9 3 viol. ✓ Clean Cc1nc(c2c(n1)n(cn2)[C@H]3[C@H]([C@@H]([C@H](O3)…
HED RCSB PDB Q836G9 154.3 Da LogP 0.35 TPSA 40.5 ✓ Ro5 ✓ Clean C(CSSCCO)O
HEJ RCSB PDB Q9Y3Z3 507.2 Da LogP -1.63 TPSA 279.1 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@H]([C@@H]([C@H](O3)C…
HF4 RCSB PDB Q9Y3Z3 483.2 Da LogP -2.21 TPSA 270.4 2 viol. ✓ Clean C1=CN(C(=O)N=C1N)[C@H]2[C@H]([C@@H]([C@H](O2)CO…
HF7 RCSB PDB Q9Y3Z3 505.2 Da LogP -0.29 TPSA 258.9 3 viol. ✓ Clean Cc1nc(c2c(n1)n(cn2)[C@H]3C[C@@H]([C@H](O3)COP(=…
HFD RCSB PDB Q9Y3Z3 525.2 Da LogP -1.49 TPSA 279.1 3 viol. ✓ Clean c1nc2c(nc(nc2n1[C@H]3[C@H]([C@@H]([C@H](O3)COP(…
MLI RCSB PDB Q836G9 102.0 Da LogP -3.12 TPSA 80.3 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(=O)[O-]
SIN RCSB PDB Q09374 118.1 Da LogP -0.06 TPSA 74.6 ✓ Ro5 ✓ Clean C(CC(=O)O)C(=O)O
T8T RCSB PDB Q9Y3Z3 523.2 Da LogP -0.37 TPSA 258.6 3 viol. ✓ Clean c1nc2c(n1[C@H]3C[C@@H]([C@H](O3)CO[P@](=O)(OP(=…
TTP RCSB PDB Q836G9 482.2 Da LogP -1.16 TPSA 244.1 2 viol. ✓ Clean CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@]…
XG4 RCSB PDB Q9Y3Z3 506.2 Da LogP -1.73 TPSA 281.7 3 viol. ✓ Clean c1nc2c(n1[C@H]3C[C@@H]([C@H](O3)CO[P@@](=O)(N[P…

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.