Protein target profile

VK055_2542

citrate-sodium symporter

Genome: KpATCC43816 Gene: AIK81139.1 citS 3D evidence: Experimental + ColabFold model UniProt P31602
Length 446
Pocket druggability 0.987
Direct ligand evidence 2 52 total records
Functional annotation 0 EC 8 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
0.7% 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
90.9 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

PDB experimental structure

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 0.987
Structure 9LSJ
Pocket Pocket 3
P2Rank 0.743
Structure 9LSK
Pocket Pocket 1
ColabFold model
FPocket 0.357 · Pocket 4
P2Rank 0.626 · Pocket 1
Core conservation Accessory gene
Roary accessory
CoreCruncher accessory
Gut microbiome 35 / 4744 genomes with a hit
Prevalence 0.7%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MTNMSQAPATEKKGVSDLLGFKIFGMPLPLYAFALITLLLSHFYNALPTDIVGGFAIMFIIGAIFGEIGKRLPIFNKYIGGAPVMIFLVAAYFVYAGIFTQKEIDAISNVMDKSNFLNLFIAVLITGAILSVNRRLLLKSLLGYIPTILMGIVGASIFGIAIGLVFGIPVDRIMMLYVLPIMGGGNGAGAVPLSEIYHSVTGRSREEYYSTAIAILTIANIFAIVFAAVLDIIGKKHTWLSGEGELVRKASFKVEEDEKAGQITHRETAVGLVLSTTCFLLAYVVAKKILPSIGGVAIHYFAWMVLIVAALNASGLCSPEIKAGAKRLSDFFSKQLLWVLMVGVGVCYTDLQEIINAITFANVVIAAIIVIGAVLGAAIGGWLMGFFPIESAITAGLCMANRGGSGDLEVLSACNRMNLISYAQISSRLGGGIVLVIASIVFGMMI

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

8 GO

Gene Ontology (GO)

8
  • GO:0008514 OBSOLETE. Enables the transfer of organic anions from one side of a membrane to the other. Organic anions are atoms or small molecules with a negative charge which contain carbon in covalent linkage.
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0015711 The directed movement of organic anions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Organic anions are atoms or small molecules with a negative charge which contain carbon in covalent linkage.
  • 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:0046872 Binding to a metal ion.
  • GO:0015293 Enables the active transport of a solute across a membrane by a mechanism whereby two or more species are transported together in the same direction in a tightly coupled process not directly linked to a form of energy other than chemiosmotic energy.
  • GO:0006101 The chemical reactions and pathways involving citrate, 2-hydroxy-1,2,3-propanetricarboxylate. Citrate is widely distributed in nature and is an important intermediate in the TCA cycle and the glyoxylate cycle.
  • GO:0006814 The directed movement of sodium ions (Na+) 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.

45 records
Show feature table
Start End DB Term Name
425 444 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
446 446 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
176 198 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
385 424 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
269 286 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
144 168 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
336 358 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
114 132 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
208 230 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
46 66 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
23 440 Pfam PF03390 2-hydroxycarboxylate transporter family
23 440 InterPro IPR004679 2-hydroxycarboxylate transporter
3 446 PIRSF PIRSF005348 YxkH
3 446 InterPro IPR004679 2-hydroxycarboxylate transporter
174 196 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
96 114 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
352 362 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
78 95 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
133 143 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
18 441 NCBIfam TIGR00783 citrate:cation symporter
18 441 InterPro IPR018025 2-hydroxycarboxylate transporter, proteobacteria/firmicutes
115 132 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
23 45 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
79 101 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
208 230 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
2 445 PANTHER PTHR40033 NA(+)-MALATE SYMPORTER
2 445 InterPro IPR004679 2-hydroxycarboxylate transporter
197 207 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
296 315 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
363 384 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
52 69 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
312 330 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
425 445 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
67 77 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
231 267 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
21 40 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
293 311 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
363 385 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
268 286 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
41 45 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
287 292 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
1 20 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
147 169 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
169 173 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
331 351 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.

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 #1
0.922
Likely same site as P2Rank 5 0.9 Å 19 shared residues 100% of smaller site
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Surrounding area
Site 2 FPocket #9
0.517
Likely same site as P2Rank 3 1.7 Å 10 shared residues 100% of smaller site
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Surrounding area
Site 3 FPocket #6
0.509
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Surrounding area
Site 4 FPocket #12
0.438
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Surrounding area

Binding pockets · P2Rank

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

Site 1 P2Rank #1
0.968
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Surrounding area
Site 2 P2Rank #2
0.737
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Surrounding area
Site 3 P2Rank #3
0.585
Likely same site as FPocket 9 1.7 Å 10 shared residues 100% of smaller site
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Surrounding area
Site 4 P2Rank #4
0.537
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Surrounding area
Site 5 P2Rank #5
0.427
Likely same site as FPocket 1 0.9 Å 19 shared residues 100% of smaller site
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Surrounding area
All structural evidence 8 experimental · 1 predicted

Structural evidence

8 + 1

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
PDB 5XAS
X-ray 3.47 Å A,B
97.3% 13-446
Viewing
PDB 5XAR
X-ray 3.62 Å A,B,C,D
97.3% 13-446
Loaded
PDB 5XAT
X-ray 3.76 Å A,B,C,D
97.3% 13-446
Loaded
PDB 5X9R
X-ray 3.98 Å A,B
97.3% 13-446
Loaded
PDB 9LSH
X-ray A Loaded
PDB 9LSI
X-ray A Loaded
PDB 9LSJ
X-ray A Loaded
PDB 9LSK
X-ray A Loaded
ColabFold VK055_2542
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 2 same-protein records
Transferred evidence 0 records from similar proteins
Structural ligands 2 2 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
BOG PDB co-crystal 292.4 Da · LogP 0.16 · TPSA 99.4 Open detail RCSB PDB
FLC PDB co-crystal Detail RCSB PDB
ZINC100034925 ZINC proposed compound · Tanimoto 1.000 Detail ZINC
ZINC100050848 ZINC proposed compound · Tanimoto 1.000 Detail ZINC
ZINC100056252 ZINC proposed compound · Tanimoto 1.000 Detail ZINC

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.

Show only:
Ligand Source crystal MW · LogP · TPSA Lipinski PAINS SMILES
BOG RCSB PDB 292.4 Da LogP 0.16 TPSA 99.4 ✓ Ro5 ✓ Clean CCCCCCCCO[C@H]1[C@@H]([C@H]([C@@H]([C@H](O1)CO)…
FLC RCSB PDB 189.1 Da LogP -5.25 TPSA 140.6 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[O-])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.