KpKP13 Protein target profile

Beta-lactamase OXA-9

Accession: KP13_01389

Gene: bla AHE47441.1 3D evidence: AlphaFold DB model + ColabFold model UniProt B2CBF6
Length 279
Pocket druggability (P2Rank · AlphaFold DB model) 0.464
Direct ligand evidence 0 56 total records
Functional annotation 1 EC 4 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 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
91.36 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) 0.464
Structure B2CBF6
Pocket Pocket 1
Druggability (FPocket) 0.475
Structure B2CBF6
Pocket Pocket 1
ColabFold model
P2Rank 0.227 · Pocket 1
FPocket 0.773 · Pocket 4
Core conservation Accessory gene
Roary accessory
CoreCruncher accessory
Gut microbiome 3 / 4744 genomes with a hit
Prevalence 0.1%

Sequence

Primary amino-acid sequence viewer.

MKDTLMKKILLLHMLVFVSATLPISSVASDEVETLKCTIIADAITGNTLYETGECARRVSPCSSFKLPLAIMGFDSGILQSPKSPTWELKPEYNPSPRDRTYKQVYPALWQSDSVVWFSQQLTSRLGVDRFTEYVKKFEYGNQDVSGDSGKHNGLTQSWLMSSLTISPKEQIQFLLRFVAHKLPVSEAAYDMAYATIPQYQAAEGWAVHGKSGSGWLRDNNGKINESRPQGWFVGWAEKNGRQVVFARLEIGKEKSDIPGGSKAREDILVELPVLMGNK

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Subcellular localization

Localization
Unknown

Enzyme Commission (EC)

1

Gene Ontology (GO)

4
  • GO:0008800 Catalysis of the reaction: a beta-lactam + H2O = a substituted beta-amino acid.
  • GO:0017001 The chemical reactions and pathways resulting in the breakdown of antibiotic, a substance produced by or derived from certain fungi, bacteria, and other organisms, that can destroy or inhibit the growth of other microorganisms.
  • GO:0008658 Binding to penicillin, an antibiotic that contains the condensed beta-lactamthiazolidine ring system.
  • GO:0046677 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 an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

16 records
Show feature table
Start End DB Term Name
26 279 Gene3D G3DSA:3.40.710.10 -
26 279 InterPro IPR012338 Beta-lactamase/transpeptidase-like
1 28 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM
1 28 SignalP_GRAM_NEGATIVE SignalP-noTM SignalP-noTM
30 279 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
22 29 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
10 21 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
38 265 SUPERFAMILY SSF56601 beta-lactamase/transpeptidase-like
38 265 InterPro IPR012338 Beta-lactamase/transpeptidase-like
61 71 ProSitePatterns PS00337 Beta-lactamase class-D active site.
61 71 InterPro IPR002137 Beta-lactamase, class-D active site
1 20 SignalP_EUK SignalP-noTM SignalP-noTM
1 29 Phobius SIGNAL_PEPTIDE Signal peptide region
48 249 Pfam PF00905 Penicillin binding protein transpeptidase domain
48 249 InterPro IPR001460 Penicillin-binding protein, transpeptidase
1 9 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.

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
0.464
Show in viewer
Surrounding area
Pocket 2 P2Rank #2
0.027
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Surrounding area
Pocket 3 P2Rank #3
0.017
Likely same site as FPocket 4 3.1 Å 8 shared residues 100% of smaller site
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Surrounding area
Pocket 4 P2Rank #4
0.003
Show in viewer
Surrounding area

Binding pockets · FPocket

Druggability (FPocket): high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Pocket 1 FPocket #1
0.475 Unusual size
Show in viewer
Surrounding area
Pocket 2 FPocket #4
0.259
Likely same site as P2Rank 3 3.1 Å 8 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_B2CBF6
AlphaFold DB full sequence Viewing
ColabFold KP13_01389
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.

56 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 8 records from similar proteins
Structural ligands 6 0 loaded crystals
Measured bioactivity 2 direct and transferred ChEMBL records
Proposed compounds 48 similarity-based ZINC candidates
Best available ligand signal
1S6 PDB via homolog 403.5 Da · LogP 1.84 · TPSA 121.5 Open detail RCSB PDB
5R7 PDB via homolog Detail RCSB PDB
DRW PDB via homolog Detail RCSB PDB
FLC PDB via homolog Detail RCSB PDB
MER 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
1S6 RCSB PDB P0A0B0 403.5 Da LogP 1.84 TPSA 121.5 ✓ Ro5 ✓ Clean Cc1c(c(no1)c2ccccc2)C(=O)N[C@H](C=O)[C@@H]3N[C@…
5R7 RCSB PDB A8FFI9 422.5 Da LogP -1.65 TPSA 171.2 ✓ Ro5 ✓ Clean C[C@H]1[C@H](C(=N[C@H]1[C@H](C=O)[C@@H](C)O)C(=…
DRW RCSB PDB P13661 422.5 Da LogP -1.65 TPSA 171.2 ✓ Ro5 ✓ Clean C[C@H]1[C@@H](C(=N[C@H]1[C@H](C=O)[C@@H](C)O)C(…
FLC RCSB PDB A8FFI9 189.1 Da LogP -5.25 TPSA 140.6 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[O-])O
MER RCSB PDB Q51400 385.5 Da LogP -0.36 TPSA 119.0 ✓ Ro5 ✓ Clean C[C@@H]1[C@@H](NC(=C1S[C@H]2C[C@H](NC2)C(=O)N(C…
NXL RCSB PDB P0A0B1 267.3 Da LogP -2.21 TPSA 139.0 ✓ Ro5 ✓ Clean C1C[C@H](N(C[C@@H]1NOS(=O)(=O)O)C=O)C(=O)N

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.