Protein target profile

KP13_00007

Ribose import ATP-binding protein rbsA

Genome: KpKP13 Gene: AHE47118.1 rbsA 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GK05
Length 511
Pocket druggability 0.692
Direct ligand evidence 0 63 total records
Functional annotation 0 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
Hit
Human identity (%)
36.264 Lower values reduce human off-target concern.
Human E-value
2.53e-06
Gut microbiome similarity
4.1% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
45.509 Higher values support similarity to known essential genes.
DEG E-value
2.82e-157 Smaller values mean stronger essential-gene similarity.

Localization

Localization
CytoplasmicMembrane

Structure confidence

ColabFold pLDDT
89.15 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 0.692
Structure A0A0H3GK05
Pocket Pocket 1
P2Rank 0.269
Structure A0A0H3GK05
Pocket Pocket 1
ColabFold model
FPocket 0.45 · Pocket 14
P2Rank 0.603 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 194 / 4744 genomes with a hit
Prevalence 4.1%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MPASRSEVAVMEALLQLKGIDKAFPGVKALSGAALNVYAGRVMALVGENGAGKSTMMKVLTGIYTRDAGSLLWLGKETTFNGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGKIDWKQMYAEADKLLAKLNLRFTSQKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESLFRVIRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVSSLDEDRLIEMMVGRKLEDQYPHLDKAPGAVRLKVDNLCGPGVDNVTFTLRQGEILGVAGLMGAGRTELMKVLYGALPRSSGSVTLDGREVVTRSPQDGLANGIVYISEDRKRDGLVLGMSVKENMSLTALRYFSRAGGSLKHKDEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGLMTRPKVLILDEPTRGVDVGAKKEIYQLINQFKADGLSIILVSSEMPEVLGMSDRIIVMHEGHLGGEFTREQATQEVLMAAAVGKLNRVNQE

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 GO

Gene Ontology (GO)

4
  • 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:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
  • GO:0015749 The process in which a monosaccharide is transported across a lipid bilayer, from one side of a membrane to the other. Monosaccharides are the simplest carbohydrates; they are polyhydric alcohols containing either an aldehyde or a keto group and between three to ten or more carbon atoms. They form the constitutional repeating units of oligo- and polysaccharides.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

25 records
Show feature table
Start End DB Term Name
266 492 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
266 492 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
39 229 SMART SM00382 AAA_5
39 229 InterPro IPR003593 AAA+ ATPase domain
287 482 SMART SM00382 AAA_5
287 482 InterPro IPR003593 AAA+ ATPase domain
267 507 FunFam G3DSA:3.40.50.300:FF:000126 Galactose/methyl galactoside import ATP-binding protein MglA
3 253 Gene3D G3DSA:3.40.50.300 -
3 253 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
15 505 ProSiteProfiles PS50893 ATP-binding cassette, ABC transporter-type domain profile.
15 505 InterPro IPR003439 ABC transporter-like, ATP-binding domain
278 433 Pfam PF00005 ABC transporter
278 433 InterPro IPR003439 ABC transporter-like, ATP-binding domain
32 179 Pfam PF00005 ABC transporter
32 179 InterPro IPR003439 ABC transporter-like, ATP-binding domain
266 507 Gene3D G3DSA:3.40.50.300 -
266 507 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
14 238 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
14 238 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
15 232 CDD cd03216 ABC_Carb_Monos_I
10 249 FunFam G3DSA:3.40.50.300:FF:000127 Ribose import ATP-binding protein RbsA
406 420 ProSitePatterns PS00211 ABC transporters family signature.
406 420 InterPro IPR017871 ABC transporter-like, conserved site
264 483 CDD cd03215 ABC_Carb_Monos_II
11 504 PANTHER PTHR43790 CARBOHYDRATE TRANSPORT ATP-BINDING PROTEIN MG119-RELATED

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.

Download VMD script Full viewer

Loading 3D structure...

Drag to rotate — click the view, then scroll to zoom.

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
0.692
Likely same site as P2Rank 2 2.3 Å 12 shared residues 92% of smaller site
Show in viewer
Surrounding area

Binding pockets · P2Rank

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

Site 1 P2Rank #1
0.269
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.247
Likely same site as FPocket 1 2.3 Å 12 shared residues 92% of smaller site
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.241
Show in viewer
Surrounding area
Site 4 P2Rank #4
0.151
Show in viewer
Surrounding area
Site 5 P2Rank #5
0.082
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_A0A0H3GK05
AlphaFold DB full sequence Viewing
ColabFold KP13_00007
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.

63 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 13 records from similar proteins
Structural ligands 13 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
AGS PDB via homolog 523.2 Da · LogP -1.51 · TPSA 262.1 Open detail RCSB PDB
ANP PDB via homolog Detail RCSB PDB
AOV PDB via homolog Detail RCSB PDB
AT4 PDB via homolog Detail RCSB PDB
CZJ 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
AGS RCSB PDB D0VWX4 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 D0VWX4 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)…
AOV RCSB PDB P0A9V1 544.2 Da LogP -3.05 TPSA 299.4 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
AT4 RCSB PDB D0VWX4 443.3 Da LogP -0.81 TPSA 212.4 2 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
CZJ RCSB PDB P0A9V1 586.6 Da LogP 3.32 TPSA 179.8 1 viol. ✓ Clean Cc1c(ccc2c1OC(=O)C(=C2O)NC(=O)C34CC5CC(C3)CC(C5…
DCQ RCSB PDB P0A9V4 322.4 Da LogP 4.49 TPSA 52.6 ✓ Ro5 Alert CCCCCCCCCCC1=C(C(=O)C(=C(C1=O)OC)OC)C
L0W RCSB PDB P0A9V4 1814.4 Da LogP 21.50 TPSA 394.5 4 viol. ✓ Clean CCCCCCCCCCCCCC(=O)O[C@H](CCCCCCCCCCC)CC(=O)O[C@…
LMD RCSB PDB P0A9V4 538.7 Da LogP 0.33 TPSA 178.5 3 viol. ✓ Clean CCCCCCCCCCCCCCO[C@H]1[C@@H]([C@H]([C@@H]([C@H](…
LMN RCSB PDB P0A9V4 1005.2 Da LogP -1.68 TPSA 357.1 3 viol. ✓ Clean CCCCCCCCCCC(CCCCCCCCCC)(CO[C@@H]1[C@@H]([C@@H](…
LMT RCSB PDB P0A9V4 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…
MMC RCSB PDB Q58663 215.6 Da LogP 0.58 TPSA 0.0 ✓ Ro5 ✓ Clean C[Hg+]
NOV RCSB PDB A0A0H3CR83 612.6 Da LogP 3.63 TPSA 200.0 2 viol. ✓ Clean Cc1c(ccc2c1OC(=O)C(=C2O)NC(=O)c3ccc(c(c3)CC=C(C…
TBU RCSB PDB Q58663 74.1 Da LogP 0.78 TPSA 20.2 ✓ Ro5 ✓ Clean CC(C)(C)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.