KpATCC43816 Protein target profile
bacterial extracellular solute-binding, 5 Middlefamily protein
Accession: VK055_0456
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
Evidence coverage
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
- 0.5% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.
Essentiality
- Essential (DEG)
- N
- DEG identity (%)
- 26.374 Higher values support similarity to known essential genes.
Structure confidence
- ColabFold pLDDT
- 92.6 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.
MSRLQQGLKTRQTRFALALKVALLGGVVAFSSAVFAEGLLKEGITPATDASQIPASAKLRKDTVVAGISEPQGIFNPYFFVNGWDENVTNVIFSRLIDWDSQGKLVPGLAESWTVSPDNKVYTIKLRPGLTFSDGSPLTAEDVAFTLTVLLDPKYDGDTDITLANIAGGTDYKAGKADSVSGLKVIDPLTLQVTTTQPGATTLAKIGGPVLSKAWYGKGYQRGNLDYLRSLHGKPLGNGPYVYDKYIPGQEIRFHANSHFYRGTPPTPRFIYRVTNPSTNFQLFQTGETDYDAFTSRPDDIEQLKMLGFANINLYGSSDYSQVEFNVHRPALQDKRVRQALIYGLDRQKLIDVVYQGYGKVAIEPIAPISWAFNAEGVNPYPYDPAQAKKLLDEAGWKAGADGIRAKDGQRLELTLLVSKKVLNDALIPIAKENWRQIGVLLKPQVVDFNALMAQRKAGNYDLASFSTSTLNDPHDGVWDFYSSEAKESGYHNAEVDKLINAGNAVLDIEQRKPIYHQLYKVLADDPPVILLGYREILSASSARVSGFKPDIYNGLTGSLPDVKIVK
Functional annotations
Enzyme classification and Gene Ontology terms linked to this protein.
Subcellular localization
- Localization
- Periplasmic
Gene Ontology (GO)
5- GO:0043190 A complex for the transport of metabolites into and out of the cell, typically comprised of four domains; two membrane-associated domains and two ATP-binding domains at the intracellular face of the membrane, that form a central pore through the plasma membrane. Each of the four core domains may be encoded as a separate polypeptide or the domains can be fused in any one of a number of ways into multidomain polypeptides. In Bacteria and Archaebacteria, ABC transporters also include substrate binding proteins to bind substrate external to the cytoplasm and deliver it to the transporter.
- GO:0055085 The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other.
- GO:0030288 The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.
- 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.
Sequence domains and features
Domain and signature matches imported from InterPro and related databases.
Show feature table
| Start | End | DB | Term | Name |
|---|---|---|---|---|
| 104 | 486 | Pfam | PF00496 | Bacterial extracellular solute-binding proteins, family 5 Middle |
| 104 | 486 | InterPro | IPR000914 | Solute-binding protein family 5 domain |
| 63 | 548 | CDD | cd00995 | PBP2_NikA_DppA_OppA_like |
| 319 | 534 | Gene3D | G3DSA:3.10.105.10 | - |
| 37 | 567 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. |
| 29 | 36 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. |
| 15 | 555 | PANTHER | PTHR30290 | PERIPLASMIC BINDING COMPONENT OF ABC TRANSPORTER |
| 15 | 555 | InterPro | IPR039424 | Solute-binding protein family 5 |
| 15 | 28 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. |
| 74 | 549 | Gene3D | G3DSA:3.40.190.10 | - |
| 13 | 35 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. |
| 20 | 559 | PIRSF | PIRSF002741 | MppA |
| 20 | 559 | InterPro | IPR030678 | Peptide/nickel binding protein, MppA-type |
| 1 | 14 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. |
| 1 | 36 | Phobius | SIGNAL_PEPTIDE | Signal peptide region |
| 93 | 225 | Gene3D | G3DSA:3.90.76.10 | - |
| 60 | 555 | SUPERFAMILY | SSF53850 | Periplasmic binding protein-like II |
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
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_A0A0H3GQV3
|
AlphaFold DB | — | — | full sequence | — | Viewing |
|
ColabFold
VK055_0456
|
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 |
|---|---|---|---|---|---|---|
| EDT RCSB PDB | Q9AL82 | 292.2 Da LogP -2.07 TPSA 155.7 | ✓ Ro5 | ✓ Clean |
C(CN(CC(=O)O)CC(=O)O)N(CC(=O)O)CC(=O)O
|
|
| GDS RCSB PDB | B8F653 | 612.6 Da LogP -3.88 TPSA 317.6 | 3 viol. | ✓ Clean |
C(CC(=O)N[C@@H](CSSC[C@@H](C(=O)NCC(=O)O)NC(=O)…
|
|
| MLI RCSB PDB | B8F653 | 102.0 Da LogP -3.12 TPSA 80.3 | ✓ Ro5 | ✓ Clean |
C(C(=O)[O-])C(=O)[O-]
|
|
| OXL RCSB PDB | Q0P844 | 88.0 Da LogP -3.51 TPSA 80.3 | ✓ Ro5 | ✓ Clean |
C(=O)(C(=O)[O-])[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 |
|---|---|---|---|---|---|
| ZINC19364242 ZINC | 1.000 | 292.2 Da LogP -2.07 TPSA 155.7 | ✓ Ro5 | ✓ Clean |
O=C(O)CN(CCN(CC(=O)O)CC(=O)O)CC(=O)O
|
| ZINC19419017 ZINC | 0.933 | 393.3 Da LogP -2.68 TPSA 196.2 | ✓ Ro5 | ✓ Clean |
O=C(O)CN(CCN(CC(=O)O)CC(=O)O)CCN(CC(=O)O)CC(=O)O
|
| ZINC22593216 ZINC | 0.933 | 494.5 Da LogP -3.30 TPSA 236.8 | 1 viol. | ✓ Clean |
O=C(O)CN(CCN(CCN(CC(=O)O)CC(=O)O)CC(=O)O)CCN(CC…
|
| ZINC31350707 ZINC | 0.767 | 349.4 Da LogP -1.86 TPSA 175.9 | ✓ Ro5 | ✓ Clean |
CC(=O)SC[C@@H](NC(=O)CC[C@@H](N)C(=O)O)C(=O)NCC…
|
| ZINC31350710 ZINC | 0.767 | 349.4 Da LogP -1.86 TPSA 175.9 | ✓ Ro5 | ✓ Clean |
CC(=O)SC[C@H](NC(=O)CC[C@@H](N)C(=O)O)C(=O)NCC(…
|
| ZINC31350713 ZINC | 0.767 | 349.4 Da LogP -1.86 TPSA 175.9 | ✓ Ro5 | ✓ Clean |
CC(=O)SC[C@@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)NCC(…
|
| ZINC3872733 ZINC | 0.767 | 336.3 Da LogP -1.72 TPSA 188.2 | ✓ Ro5 | ✓ Clean |
N[C@H](CCC(=O)N[C@@H](CSN=O)C(=O)NCC(=O)O)C(=O)O
|
| ZINC3872734 ZINC | 0.767 | 336.3 Da LogP -1.72 TPSA 188.2 | ✓ Ro5 | ✓ Clean |
N[C@H](CCC(=O)N[C@H](CSN=O)C(=O)NCC(=O)O)C(=O)O
|
| ZINC4544082 ZINC | 0.767 | 335.4 Da LogP -1.38 TPSA 158.8 | ✓ Ro5 | ✓ Clean |
CCSC[C@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)NCC(=O)O
|
| ZINC4544083 ZINC | 0.767 | 335.4 Da LogP -1.38 TPSA 158.8 | ✓ Ro5 | ✓ Clean |
CCSC[C@@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)NCC(=O)O
|
| ZINC1769289 ZINC | 0.765 | 306.3 Da LogP -1.68 TPSA 155.7 | ✓ Ro5 | ✓ Clean |
O=C(O)CN(CCCN(CC(=O)O)CC(=O)O)CC(=O)O
|
| ZINC4683946 ZINC | 0.765 | 320.3 Da LogP -1.29 TPSA 155.7 | ✓ Ro5 | ✓ Clean |
O=C(O)CN(CCCCN(CC(=O)O)CC(=O)O)CC(=O)O
|
| ZINC19364891 ZINC | 0.737 | 204.2 Da LogP -0.98 TPSA 81.1 | ✓ Ro5 | ✓ Clean |
CN(C)CCN(CC(=O)O)CC(=O)O
|
| ZINC19364892 ZINC | 0.737 | 232.3 Da LogP -0.20 TPSA 81.1 | ✓ Ro5 | ✓ Clean |
CCN(CC)CCN(CC(=O)O)CC(=O)O
|
| ZINC19366122 ZINC | 0.737 | 278.3 Da LogP -2.16 TPSA 138.6 | ✓ Ro5 | ✓ Clean |
O=C(O)CN(CCO)CCN(CC(=O)O)CC(=O)O
|
| ZINC33806192 ZINC | 0.737 | 320.3 Da LogP -1.29 TPSA 155.7 | ✓ Ro5 | ✓ Clean |
O=C(O)CCN(CCC(=O)O)CCN(CC(=O)O)CC(=O)O
|
| ZINC5908834 ZINC | 0.737 | 379.3 Da LogP -2.09 TPSA 196.2 | ✓ Ro5 | ✓ Clean |
O=C(O)CN(CCN(CCN(CC(=O)O)CC(=O)O)C(=O)O)CC(=O)O
|
| ZINC2554974 ZINC | 0.732 | 289.3 Da LogP -1.73 TPSA 158.8 | ✓ Ro5 | ✓ Clean |
CC[C@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)NCC(=O)O
|
| ZINC3830891 ZINC | 0.732 | 307.3 Da LogP -2.21 TPSA 158.8 | 1 viol. | ✓ Clean |
N[C@@H](CCC(=O)N[C@@H](CS)C(=O)NCC(=O)O)C(=O)O
|
| ZINC3830892 ZINC | 0.732 | 307.3 Da LogP -2.21 TPSA 158.8 | 1 viol. | ✓ Clean |
N[C@@H](CCC(=O)N[C@H](CS)C(=O)NCC(=O)O)C(=O)O
|
| ZINC3830893 ZINC | 0.732 | 307.3 Da LogP -2.21 TPSA 158.8 | 1 viol. | ✓ Clean |
N[C@H](CCC(=O)N[C@@H](CS)C(=O)NCC(=O)O)C(=O)O
|
| ZINC3830894 ZINC | 0.732 | 307.3 Da LogP -2.21 TPSA 158.8 | 1 viol. | ✓ Clean |
N[C@H](CCC(=O)N[C@H](CS)C(=O)NCC(=O)O)C(=O)O
|
| ZINC2527900 ZINC | 0.722 | 205.2 Da LogP -1.07 TPSA 115.1 | ✓ Ro5 | ✓ Clean |
O=C(O)CCN(CC(=O)O)CC(=O)O
|
| ZINC4261886 ZINC | 0.722 | 348.4 Da LogP -0.51 TPSA 155.7 | ✓ Ro5 | ✓ Clean |
O=C(O)CN(CCCCCCN(CC(=O)O)CC(=O)O)CC(=O)O
|
| ZINC22057269 ZINC | 0.702 | 406.5 Da LogP -0.94 TPSA 179.1 | ✓ Ro5 | ✓ Clean |
CCN(CC)C(=O)SC[C@H](NC(=O)CC[C@H](N)C(=O)O)C(=O…
|
| ZINC35997292 ZINC | 0.702 | 406.5 Da LogP -0.94 TPSA 179.1 | ✓ Ro5 | ✓ Clean |
CCN(CC)C(=O)SC[C@H](NC(=O)CC[C@@H](N)C(=O)O)C(=…
|
| ZINC4534315 ZINC | 0.702 | 363.4 Da LogP -0.60 TPSA 158.8 | ✓ Ro5 | ✓ Clean |
CCCCSC[C@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)NCC(=O)O
|
| ZINC98091813 ZINC | 0.702 | 406.5 Da LogP -0.94 TPSA 179.1 | ✓ Ro5 | ✓ Clean |
CCN(CC)C(=O)SC[C@@H](NC(=O)CC[C@H](N)C(=O)O)C(=…
|
| ZINC98091814 ZINC | 0.702 | 406.5 Da LogP -0.94 TPSA 179.1 | ✓ Ro5 | ✓ Clean |
CCN(CC)C(=O)SC[C@@H](NC(=O)CC[C@@H](N)C(=O)O)C(…
|
| ZINC149813449 ZINC | 0.700 | 278.2 Da LogP -1.48 TPSA 155.7 | ✓ Ro5 | ✓ Clean |
O=C(O)CN(CCN(CC(=O)O)C(=O)O)CC(=O)O
|
| ZINC22576460 ZINC | 0.684 | 320.3 Da LogP -1.29 TPSA 155.7 | ✓ Ro5 | ✓ Clean |
O=C(O)CCN(CCN(CCC(=O)O)CC(=O)O)CC(=O)O
|
| ZINC1616624 ZINC | 0.682 | 355.3 Da LogP -3.25 TPSA 213.2 | 1 viol. | ✓ Clean |
N[C@@H](CCC(=O)N[C@@H](CS(=O)(=O)O)C(=O)NCC(=O)…
|
| ZINC1616625 ZINC | 0.682 | 355.3 Da LogP -3.25 TPSA 213.2 | 1 viol. | ✓ Clean |
N[C@@H](CCC(=O)N[C@H](CS(=O)(=O)O)C(=O)NCC(=O)O…
|
| ZINC1616626 ZINC | 0.682 | 355.3 Da LogP -3.25 TPSA 213.2 | 1 viol. | ✓ Clean |
N[C@H](CCC(=O)N[C@@H](CS(=O)(=O)O)C(=O)NCC(=O)O…
|
| ZINC1616627 ZINC | 0.682 | 355.3 Da LogP -3.25 TPSA 213.2 | 1 viol. | ✓ Clean |
N[C@H](CCC(=O)N[C@H](CS(=O)(=O)O)C(=O)NCC(=O)O)…
|
| ZINC14880561 ZINC | 0.673 | 419.5 Da LogP 0.96 TPSA 158.8 | ✓ Ro5 | ✓ Clean |
CCCCCCCCSC[C@@H](NC(=O)CC[C@@H](N)C(=O)O)C(=O)N…
|
| ZINC14880563 ZINC | 0.673 | 419.5 Da LogP 0.96 TPSA 158.8 | ✓ Ro5 | ✓ Clean |
CCCCCCCCSC[C@H](NC(=O)CC[C@@H](N)C(=O)O)C(=O)NC…
|
| ZINC14880565 ZINC | 0.673 | 419.5 Da LogP 0.96 TPSA 158.8 | ✓ Ro5 | ✓ Clean |
CCCCCCCCSC[C@@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)NC…
|
| ZINC3874923 ZINC | 0.673 | 391.5 Da LogP 0.18 TPSA 158.8 | ✓ Ro5 | ✓ Clean |
CCCCCCSC[C@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)NCC(=…
|
| ZINC3874924 ZINC | 0.673 | 391.5 Da LogP 0.18 TPSA 158.8 | ✓ Ro5 | ✓ Clean |
CCCCCCSC[C@@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)NCC(…
|
| ZINC3874925 ZINC | 0.673 | 391.5 Da LogP 0.18 TPSA 158.8 | ✓ Ro5 | ✓ Clean |
CCCCCCSC[C@H](NC(=O)CC[C@@H](N)C(=O)O)C(=O)NCC(…
|
| ZINC3874926 ZINC | 0.673 | 391.5 Da LogP 0.18 TPSA 158.8 | ✓ Ro5 | ✓ Clean |
CCCCCCSC[C@@H](NC(=O)CC[C@@H](N)C(=O)O)C(=O)NCC…
|
| ZINC90669676 ZINC | 0.667 | 377.4 Da LogP -2.57 TPSA 176.0 | ✓ Ro5 | ✓ Clean |
O=CCN(CCN(CC(=O)O)CC(=O)O)CCN(CC(=O)O)CC(=O)O
|
| ZINC2390999 ZINC | 0.655 | 275.3 Da LogP -1.99 TPSA 172.8 | ✓ Ro5 | ✓ Clean |
NC(=O)CC[C@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)O
|
| ZINC22052182 ZINC | 0.650 | 336.3 Da LogP -2.05 TPSA 164.9 | ✓ Ro5 | ✓ Clean |
O=C(O)CN(CCOCCN(CC(=O)O)CC(=O)O)CC(=O)O
|
| ZINC4962382 ZINC | 0.647 | 425.5 Da LogP -0.52 TPSA 175.9 | ✓ Ro5 | ✓ Clean |
N[C@H](CCC(=O)N[C@@H](CSCC(=O)c1ccccc1)C(=O)NCC…
|
| ZINC4962383 ZINC | 0.647 | 425.5 Da LogP -0.52 TPSA 175.9 | ✓ Ro5 | ✓ Clean |
N[C@H](CCC(=O)N[C@H](CSCC(=O)c1ccccc1)C(=O)NCC(…
|
| ZINC4962414 ZINC | 0.647 | 439.5 Da LogP -0.13 TPSA 175.9 | ✓ Ro5 | ✓ Clean |
N[C@@H](CCC(=O)N[C@H](CSCCC(=O)c1ccccc1)C(=O)NC…
|
| ZINC4962415 ZINC | 0.647 | 439.5 Da LogP -0.13 TPSA 175.9 | ✓ Ro5 | ✓ Clean |
N[C@H](CCC(=O)N[C@@H](CSCCC(=O)c1ccccc1)C(=O)NC…
|
| ZINC4962416 ZINC | 0.647 | 439.5 Da LogP -0.13 TPSA 175.9 | ✓ Ro5 | ✓ Clean |
N[C@H](CCC(=O)N[C@H](CSCCC(=O)c1ccccc1)C(=O)NCC…
|
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.