Protein target profile

KP13_32345

SbmA

Genome: KpKP13 Gene: AHE46098.1 sbmA 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GIY6
Length 406
Pocket druggability 0.988
Direct ligand evidence 0 52 total records
Functional annotation 0 EC 5 GO
Target summary

Strong target candidate with converging metabolic, structural and chemical evidence.

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
1.9% 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
CytoplasmicMembrane

Structure confidence

ColabFold pLDDT
90.1 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 0.988
Structure A0A0H3GIY6
Pocket Pocket 3
P2Rank 0.991
Structure A0A0H3GIY6
Pocket Pocket 1
ColabFold model
FPocket 0.995 · Pocket 31
P2Rank 0.991 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 90 / 4744 genomes with a hit
Prevalence 1.9%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MFKSFFPKPGPFFISAFIWSLLAVIFWQAGGGDWLLRVTGASQNVAISAARFWSLNYLVFYAYYLFCVGVFALFWFVYCPHRWQYWSILGTSLIIFVTWFLVEVGVAINAWYAPFYDLIQSALATPHKVSINQFYQEIGVFLGIAIIAVIIGVMNNFFVSHYVFRWRTAMNEHYMAHWQHLRHIEGAAQRVQEDTMRFASTLEDMGVSFINAVMTLIAFLPVLVTLSEHVPDLPIVGHLPYGLVIAAIVWSLMGTGLLAVVGIKLPGLEFKNQRVEAAYRKELVYGEDDETRATPPTVRELFRAVRRNYFRLYFHYMYFNIARILYLQVDNVFGLFLLFPSIVAGTITLGLMTQITNVFGQVRGSFQYLISSWTTLVELMSIYKRLRSFERELDGKPLQEAIPTLR

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

Gene Ontology (GO)

5
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:1904680 Enables the transfer of a peptide from one side of a membrane to the other.
  • GO:0015833 The directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
  • GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

34 records
Show feature table
Start End DB Term Name
138 160 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
354 364 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
309 326 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
165 205 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
80 393 Pfam PF05992 SbmA/BacA-like family
80 393 InterPro IPR009248 SbmA/BacA-like
327 331 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
79 84 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
384 406 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
12 30 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
206 227 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
264 308 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
85 112 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
239 263 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
93 394 PANTHER PTHR11384 ATP-BINDING CASSETTE, SUB-FAMILY D MEMBER
228 238 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
365 383 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
332 353 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
331 353 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
309 327 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
57 79 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
138 164 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
113 137 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
1 11 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
241 263 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
86 108 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
71 392 Gene3D G3DSA:1.20.1560.10 ABC transporter type 1, transmembrane domain
71 392 InterPro IPR036640 ABC transporter type 1, transmembrane domain superfamily
207 226 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
12 31 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
58 78 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
31 57 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
80 390 SUPERFAMILY SSF90123 ABC transporter transmembrane region
80 390 InterPro IPR036640 ABC transporter type 1, transmembrane domain superfamily

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 #3
0.988
Likely same site as P2Rank 1 2.1 Å 30 shared residues 97% of smaller site
Unusual size
Show in viewer
Surrounding area
Site 2 FPocket #27
0.216
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
0.991
Likely same site as FPocket 3 2.1 Å 30 shared residues 97% of smaller site
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.133
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.092
Show in viewer
Surrounding area
Site 4 P2Rank #4
0.077
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Surrounding area
Site 5 P2Rank #5
0.057
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_A0A0H3GIY6
AlphaFold DB full sequence Viewing
ColabFold KP13_32345
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.

52 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 2 records from similar proteins
Structural ligands 2 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
LMT PDB via homolog Detail RCSB PDB
ZINC100053689 ZINC proposed compound · Tanimoto 1.000 Detail ZINC
ZINC100053691 ZINC proposed compound · Tanimoto 1.000 Detail ZINC
ZINC1501015302 ZINC proposed compound · Tanimoto 1.000 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 P9WQI9 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)…
LMT RCSB PDB P9WQI9 510.6 Da LogP -0.45 TPSA 178.5 3 viol. ✓ Clean CCCCCCCCCCCCO[C@H]1[C@@H]([C@H]([C@@H]([C@H](O1…

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.