KpKP13 Protein target profile
sn-glycerol-3-phosphate-binding periplasmic protein ugpB
Accession: KP13_00647
Promising target candidate with multiple supporting evidence streams.
Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.
Main supporting evidence
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
- 2.6% 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
- 94.69 0-100 confidence; >70 supports local structural interpretation.
Binding-site evidence
AlphaFold DB / UniProt modelP2Rank'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.
Sequence
Primary amino-acid sequence viewer.
MISLRHTALGLALSLAFAGQALAVTTIPFWHSMEGELGKEVDSLAQRFNAANPDYKIVPVYKGNYEQSLSAGIAAFRTGNAPAILQVYEVGTATMMASKAIKPVYQVFSEAGIKFDESQFVPTVAGYYTDSKTGHLLSQPFNSSTPVLYYNKDAFKKAGLDPEQPPKTWQDLAAYTAKLKAAGMKCGYASGWQGWIQIENFSAWHGLPVATKNNGFDGTDAVLEFNKPEQVKHIALLEEMNKKGDFSYFGRKDESTEKFYNGDCAITTASSGSLADIRQYAKFNYGVGMMPYDADVKGAPQNAIIGGASLWVMQGKDKETYTGVAKFLDFLTKPENAAEWHQKTGYLPITTAAYDLTRQQGFYDKNPGADIATRQMLNKPPLPFTKGLRLGNMPQIRTIVDEELESVWTGKKTPQQALDSAVQRGNQLLRRFEQATKS
Functional annotations
Enzyme classification and Gene Ontology terms linked to this protein.
Subcellular localization
- Localization
- Periplasmic
Gene Ontology (GO)
1- GO:0055085 The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other.
Sequence domains and features
Domain and signature matches imported from InterPro and related databases.
Show feature table
| Start | End | DB | Term | Name |
|---|---|---|---|---|
| 25 | 425 | SUPERFAMILY | SSF53850 | Periplasmic binding protein-like II |
| 26 | 424 | CDD | cd14748 | PBP2_UgpB |
| 1 | 23 | Phobius | SIGNAL_PEPTIDE | Signal peptide region |
| 1 | 23 | SignalP_EUK | SignalP-noTM | SignalP-noTM |
| 5 | 392 | PANTHER | PTHR43649 | ARABINOSE-BINDING PROTEIN-RELATED |
| 145 | 424 | Gene3D | G3DSA:3.40.190.10 | - |
| 1 | 6 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. |
| 24 | 438 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. |
| 7 | 18 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. |
| 7 | 29 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. |
| 29 | 383 | Gene3D | G3DSA:3.40.190.10 | - |
| 140 | 157 | ProSitePatterns | PS01037 | Bacterial extracellular solute-binding proteins, family 1 signature. |
| 140 | 157 | InterPro | IPR006061 | Solute-binding family 1, conserved site |
| 1 | 23 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM |
| 19 | 23 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. |
| 44 | 366 | Pfam | PF13416 | Bacterial extracellular solute-binding protein |
| 44 | 366 | InterPro | IPR006059 | Bacterial extracellular solute-binding protein |
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.
How colors and pocket overlays are used
Pocket details Inspect a specific pocket, or open the full viewer
- Method
- -
- Score
- -
- Visible layer
- -
- Residues
- -
- Pocket properties
- -
Selecting a pocket opens its details and centers the viewer without clearing other active layers. Use Focus this pocket when you want to hide the rest; use Surface for the wider residue environment.
Binding pockets · P2Rank
Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2
Binding pockets · FPocket
Druggability (FPocket): high ≥ 0.7 · medium 0.4–0.69 · low < 0.4
Binding pockets · P2Rank
Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2
Binding pockets · FPocket
Druggability (FPocket): high ≥ 0.7 · medium 0.4–0.69 · low < 0.4
All structural evidence
Structural evidence
0 + 2Experimental 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_A0A0H3H458
|
AlphaFold DB | — | — | full sequence | — | Viewing |
|
ColabFold
KP13_00647
|
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.
Structural ligand evidence is available for this target.
Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in Target, use Open crystal to inspect it in the structure viewer.
No PDB structure with a co-crystallized ligand found for this exact protein.
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.
| Ligand | Source crystal | UniProt (homolog) | MW · LogP · TPSA | Lipinski | PAINS | SMILES |
|---|---|---|---|---|---|---|
| BGQ RCSB PDB | Q53W80 | 105.1 Da LogP -0.84 TPSA 60.4 | ✓ Ro5 | ✓ Clean |
C(CO)[C@H](C[O])O
|
|
| CH5 RCSB PDB | P71619 | 258.2 Da LogP -0.82 TPSA 96.2 | ✓ Ro5 | ✓ Clean |
C[N+](C)(C)CCO[P@](=O)(O)OC[C@@H](CO)O
|
|
| CO2 RCSB PDB | Q53W80 | 44.0 Da LogP -0.58 TPSA 34.1 | ✓ Ro5 | ✓ Clean |
C(=O)=O
|
|
| FGO RCSB PDB | Q5SLB4 | 629.5 Da LogP -3.39 TPSA 299.6 | 3 viol. | ✓ Clean |
c1nc2c(n1[C@H]3[C@@H]4CC(C[C@@H]4[C@H](O3)COP(=…
|
|
| G3P RCSB PDB | P0AG80 | 172.1 Da LogP -1.55 TPSA 107.2 | ✓ Ro5 | ✓ Clean |
C([C@H](COP(=O)(O)O)O)O
|
|
| MRY RCSB PDB | Q53W80 | 122.1 Da LogP -2.31 TPSA 80.9 | ✓ Ro5 | ✓ Clean |
C([C@H]([C@H](CO)O)O)O
|
|
| P33 RCSB PDB | Q53W80 | 326.4 Da LogP -0.93 TPSA 95.8 | ✓ Ro5 | ✓ Clean |
C(COCCOCCOCCOCCOCCOCCO)O
|
|
| PO2 RCSB PDB | Q5SLB4 | 63.0 Da LogP -0.45 TPSA 40.1 | ✓ Ro5 | ✓ Clean |
[O-]P=O
|
|
| PO3 RCSB PDB | Q5SLB4 | 79.0 Da LogP -1.64 TPSA 63.2 | ✓ Ro5 | ✓ Clean |
[O-][P-](=O)[O-]
|
|
| SO2 RCSB PDB | Q53W80 | 64.1 Da LogP -0.67 TPSA 34.1 | ✓ Ro5 | ✓ Clean |
O=S=O
|
Experimental bioactivity from ChEMBL measured directly on this protein. Score = pchembl (−log Ki/IC₅₀; higher = more potent).
No ChEMBL bioactivity data found for this exact protein.
Bioactivity inferred from similar proteins in ChEMBL. Score = pchembl (−log Ki/IC₅₀; higher = more potent).
No ChEMBL hits found through similar proteins.
Proposed virtual-screening candidates from ZINC. Score = Tanimoto similarity to a known binder (0–1; higher = more similar).
| Ligand | Tanimoto | MW · LogP · TPSA | Lipinski | PAINS | SMILES |
|---|---|---|---|---|---|
| ZINC12501520 ZINC | 1.000 | 458.5 Da LogP -0.88 TPSA 123.5 | 1 viol. | ✓ Clean |
OCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO
|
| ZINC3874716 ZINC | 1.000 | 414.5 Da LogP -0.90 TPSA 114.3 | ✓ Ro5 | ✓ Clean |
OCCOCCOCCOCCOCCOCCOCCOCCOCCO
|
| ZINC4283769 ZINC | 1.000 | 238.3 Da LogP -0.96 TPSA 77.4 | ✓ Ro5 | ✓ Clean |
OCCOCCOCCOCCOCCO
|
| ZINC4521548 ZINC | 1.000 | 282.3 Da LogP -0.95 TPSA 86.6 | ✓ Ro5 | ✓ Clean |
OCCOCCOCCOCCOCCOCCO
|
| ZINC5178829 ZINC | 1.000 | 326.4 Da LogP -0.93 TPSA 95.8 | ✓ Ro5 | ✓ Clean |
OCCOCCOCCOCCOCCOCCOCCO
|
| ZINC5178830 ZINC | 1.000 | 370.4 Da LogP -0.91 TPSA 105.1 | ✓ Ro5 | ✓ Clean |
OCCOCCOCCOCCOCCOCCOCCOCCO
|
| ZINC1529618 ZINC | 0.739 | 246.2 Da LogP -2.17 TPSA 136.7 | ✓ Ro5 | ✓ Clean |
O=P(O)(OC[C@@H](O)CO)OC[C@H](O)CO
|
| ZINC1529620 ZINC | 0.739 | 246.2 Da LogP -2.17 TPSA 136.7 | ✓ Ro5 | ✓ Clean |
O=P(O)(OC[C@@H](O)CO)OC[C@@H](O)CO
|
| ZINC115086873 ZINC | 0.688 | 209.2 Da LogP -1.08 TPSA 83.2 | ✓ Ro5 | ✓ Clean |
NOCCOCCOCCOCCO
|
| ZINC137432264 ZINC | 0.688 | 457.6 Da LogP -0.91 TPSA 129.3 | 1 viol. | ✓ Clean |
NCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO
|
| ZINC146143823 ZINC | 0.688 | 237.3 Da LogP -1.00 TPSA 83.2 | ✓ Ro5 | ✓ Clean |
NCCOCCOCCOCCOCCO
|
| ZINC1542984442 ZINC | 0.688 | 413.5 Da LogP -0.93 TPSA 120.1 | ✓ Ro5 | ✓ Clean |
NCCOCCOCCOCCOCCOCCOCCOCCOCCO
|
| ZINC1565503710 ZINC | 0.688 | 254.3 Da LogP -0.03 TPSA 57.2 | ✓ Ro5 | ✓ Clean |
OCCOCCOCCOCCOCCS
|
| ZINC1580161 ZINC | 0.688 | 208.3 Da LogP -0.33 TPSA 57.2 | ✓ Ro5 | ✓ Clean |
COCCOCCOCCOCCO
|
| ZINC16052118 ZINC | 0.688 | 340.4 Da LogP -0.28 TPSA 84.8 | ✓ Ro5 | ✓ Clean |
COCCOCCOCCOCCOCCOCCOCCO
|
| ZINC16052257 ZINC | 0.688 | 384.5 Da LogP -0.26 TPSA 94.1 | ✓ Ro5 | ✓ Clean |
COCCOCCOCCOCCOCCOCCOCCOCCO
|
| ZINC1857792028 ZINC | 0.688 | 430.6 Da LogP 0.04 TPSA 94.1 | ✓ Ro5 | ✓ Clean |
OCCOCCOCCOCCOCCOCCOCCOCCOCCS
|
| ZINC1857792057 ZINC | 0.688 | 474.6 Da LogP 0.06 TPSA 103.3 | 1 viol. | ✓ Clean |
OCCOCCOCCOCCOCCOCCOCCOCCOCCOCCS
|
| ZINC230494776 ZINC | 0.688 | 325.4 Da LogP -0.96 TPSA 101.6 | ✓ Ro5 | ✓ Clean |
NCCOCCOCCOCCOCCOCCOCCO
|
| ZINC34317654 ZINC | 0.688 | 472.6 Da LogP -0.23 TPSA 112.5 | 1 viol. | ✓ Clean |
COCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO
|
| ZINC38917157 ZINC | 0.688 | 210.3 Da LogP -0.04 TPSA 47.9 | ✓ Ro5 | ✓ Clean |
OCCOCCOCCOCCS
|
| ZINC44076059 ZINC | 0.688 | 428.5 Da LogP -0.24 TPSA 103.3 | ✓ Ro5 | ✓ Clean |
COCCOCCOCCOCCOCCOCCOCCOCCOCCO
|
| ZINC5210101 ZINC | 0.688 | 252.3 Da LogP -0.31 TPSA 66.4 | ✓ Ro5 | ✓ Clean |
COCCOCCOCCOCCOCCO
|
| ZINC5650743 ZINC | 0.688 | 222.3 Da LogP 0.07 TPSA 57.2 | ✓ Ro5 | ✓ Clean |
CCOCCOCCOCCOCCO
|
| ZINC5997860 ZINC | 0.688 | 296.4 Da LogP -0.29 TPSA 75.6 | ✓ Ro5 | ✓ Clean |
COCCOCCOCCOCCOCCOCCO
|
| ZINC6403917 ZINC | 0.688 | 354.4 Da LogP 0.11 TPSA 84.8 | ✓ Ro5 | ✓ Clean |
CCOCCOCCOCCOCCOCCOCCOCCO
|
| ZINC77271182 ZINC | 0.688 | 281.3 Da LogP -0.98 TPSA 92.4 | ✓ Ro5 | ✓ Clean |
NCCOCCOCCOCCOCCOCCO
|
| ZINC83253921 ZINC | 0.688 | 369.5 Da LogP -0.95 TPSA 110.9 | ✓ Ro5 | ✓ Clean |
NCCOCCOCCOCCOCCOCCOCCOCCO
|
| ZINC90741446 ZINC | 0.688 | 386.5 Da LogP 0.02 TPSA 84.8 | ✓ Ro5 | ✓ Clean |
OCCOCCOCCOCCOCCOCCOCCOCCS
|
| ZINC90741447 ZINC | 0.688 | 298.4 Da LogP -0.01 TPSA 66.4 | ✓ Ro5 | ✓ Clean |
OCCOCCOCCOCCOCCOCCS
|
| ZINC144169243 ZINC | 0.647 | 281.3 Da LogP -1.37 TPSA 89.4 | ✓ Ro5 | ✓ Clean |
OCCOCCOCCNCCOCCOCCO
|
| ZINC205758716 ZINC | 0.647 | 457.6 Da LogP -1.31 TPSA 126.3 | 1 viol. | ✓ Clean |
OCCOCCOCCOCCOCCNCCOCCOCCOCCOCCO
|
| ZINC575441396 ZINC | 0.647 | 369.5 Da LogP -1.34 TPSA 107.9 | ✓ Ro5 | ✓ Clean |
OCCOCCOCCOCCNCCOCCOCCOCCO
|
| ZINC5975509 ZINC | 0.640 | 202.1 Da LogP -2.19 TPSA 127.5 | ✓ Ro5 | ✓ Clean |
O=P(O)(O)OC[C@H](O)[C@H](O)CO
|
| ZINC12503440 ZINC | 0.620 | 363.2 Da LogP -2.57 TPSA 206.0 | 1 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@@H]2O[C@H](CO)[C@@H](OP(=O)(O)O)…
|
| ZINC1530370 ZINC | 0.620 | 363.2 Da LogP -2.57 TPSA 206.0 | 1 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@H]2O[C@@H](CO)[C@H](OP(=O)(O)O)[…
|
| ZINC28631009 ZINC | 0.620 | 363.2 Da LogP -2.57 TPSA 206.0 | 1 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@@H]2O[C@H](CO)[C@H](OP(=O)(O)O)[…
|
| ZINC3872740 ZINC | 0.620 | 363.2 Da LogP -2.57 TPSA 206.0 | 1 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@H]2O[C@@H](CO)[C@@H](OP(=O)(O)O)…
|
| ZINC3872741 ZINC | 0.620 | 363.2 Da LogP -2.57 TPSA 206.0 | 1 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@@H]2O[C@@H](CO)[C@@H](OP(=O)(O)O…
|
| ZINC3872742 ZINC | 0.620 | 363.2 Da LogP -2.57 TPSA 206.0 | 1 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@H]2O[C@@H](CO)[C@@H](OP(=O)(O)O)…
|
| ZINC3872743 ZINC | 0.620 | 363.2 Da LogP -2.57 TPSA 206.0 | 1 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@@H]2O[C@@H](CO)[C@@H](OP(=O)(O)O…
|
| ZINC100055463 ZINC | 0.615 | 212.2 Da LogP -4.22 TPSA 141.6 | 1 viol. | ✓ Clean |
OC[C@H](O)[C@@H](O)[C@H](O)[C@H](O)[C@H](O)CO
|
| ZINC100064885 ZINC | 0.615 | 212.2 Da LogP -4.22 TPSA 141.6 | 1 viol. | ✓ Clean |
OC[C@H](O)[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)CO
|
| ZINC17780060 ZINC | 0.615 | 212.2 Da LogP -4.22 TPSA 141.6 | 1 viol. | ✓ Clean |
OC[C@@H](O)[C@H](O)C(O)[C@H](O)[C@H](O)CO
|
| ZINC17952732 ZINC | 0.615 | 212.2 Da LogP -4.22 TPSA 141.6 | 1 viol. | ✓ Clean |
OC[C@H](O)[C@@H](O)C(O)[C@H](O)[C@H](O)CO
|
| ZINC18042331 ZINC | 0.615 | 242.2 Da LogP -4.86 TPSA 161.8 | 1 viol. | ✓ Clean |
OC[C@H](O)[C@H](O)[C@H](O)[C@H](O)[C@H](O)[C@H]…
|
| ZINC18120313 ZINC | 0.615 | 212.2 Da LogP -4.22 TPSA 141.6 | 1 viol. | ✓ Clean |
OC[C@H](O)[C@H](O)C(O)[C@H](O)[C@H](O)CO
|
| ZINC3979006 ZINC | 0.615 | 212.2 Da LogP -4.22 TPSA 141.6 | 1 viol. | ✓ Clean |
OC[C@@H](O)[C@@H](O)C(O)[C@H](O)[C@H](O)CO
|
| ZINC4403105 ZINC | 0.615 | 242.2 Da LogP -4.86 TPSA 161.8 | 1 viol. | ✓ Clean |
OC[C@H](O)[C@@H](O)[C@H](O)[C@H](O)[C@H](O)[C@H…
|
| ZINC4403107 ZINC | 0.615 | 242.2 Da LogP -4.86 TPSA 161.8 | 1 viol. | ✓ Clean |
OC[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)[C@H](O)[C@…
|
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.